Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T17967 | Target Info | |||
| Target Name | Pyruvate dehydrogenase kinase 2 (PDHK2) | ||||
| Synonyms | PDKII; PDK2; PDH kinase 2; [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | PDK2 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Adenosine triphosphate | Ligand Info | |||||
| Structure Description | crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands | PDB:2BU2 | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [1] |
| PDB Sequence |
GSAPKYIEHF
15 SKFSPSPLSM25 KQFLDFSNAC37 EKTSFTFLRQ47 ELPVRLANIM57 KEINLLPDRV 67 LSTPSVQLVQ77 SWYVQSLLDI87 MEFLDKDPED97 HRTLSQFTDA107 LVTIRNRHND 117 VVPTMAQGVL127 EYKDTYGDDP137 VSNQNIQYFL147 DRFYLSRISI157 RMLINQHTLI 167 FDPKHIGSID184 PNCNVSEVVK194 DAYDMAKLLC204 DKYYMASPDL214 EIQEINAANS 224 KQPIHMVYVP234 SHLYHMLFEL244 FKNAMRATVE254 SHESSLILPP264 IKVMVALGEE 274 DLSIKMSDRG284 GGVPLRKIER294 LFSYMYSTLA316 GFGYGLPISR326 LYAKYFQGDL 336 QLFSMEGFGT346 DAVIYLKALS356 TDSVERLPVY366 NKSAWRHYQT376 IQEAGDWCV |
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|
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GLU243
3.577
LYS246
4.127
ASN247
3.008
ALA248
3.971
ARG250
3.223
ALA251
3.306
ASP282
2.898
GLY284
4.693
GLY286
4.304
VAL287
3.290
LEU295
2.986
|
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| Ligand Name: TF2 | Ligand Info | |||||
| Structure Description | crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands | PDB:2BU6 | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [1] |
| PDB Sequence |
GSAPKYIEHF
15 SKFSPSPLSM25 KQFLDFACEK39 TSFTFLRQEL49 PVRLANIMKE59 INLLPDRVLS 69 TPSVQLVQSW79 YVQSLLDIME89 FLDKDPEDHR99 TLSQFTDALV109 TIRNRHNDVV 119 PTMAQGVLEY129 KDTYGDDPVS139 NQNIQYFLDR149 FYLSRISIRM159 LINQHTLIFD 169 KHIGSIDPNC187 NVSEVVKDAY197 DMAKLLCDKY207 YMASPDLEIQ217 EINAANSKQP 227 IHMVYVPSHL237 YHMLFELFKN247 AMRATVESHE257 SSLILPPIKV267 MVALGEEDLS 277 IKMSDRGGGV287 PLRKIERLFS297 YMYSTAPGYG321 LPISRLYAKY331 FQGDLQLFSM 341 EGFGTDAVIY351 LKALSTDSVE361 RLPVYNKSAW371 RHYQTIQEAG381 DWCV |
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| Ligand Name: adenosine diphosphate | Ligand Info | |||||
| Structure Description | crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands | PDB:2BU8 | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [1] |
| PDB Sequence |
GSAPKYIEHF
15 SKFSPSPLSM25 KQFLDFGSSN35 ACEKTSFTFL45 RQELPVRLAN55 IMKEINLLPD 65 RVLSTPSVQL75 VQSWYVQSLL85 DIMEFLDKDP95 EDHRTLSQFT105 DALVTIRNRH 115 NDVVPTMAQG125 VLEYKDTYGD135 DPVSNQNIQY145 FLDRFYLSRI155 SIRMLINQHT 165 LIFDGSTNPA175 HPKHIGSIDP185 NCNVSEVVKD195 AYDMAKLLCD205 KYYMASPDLE 215 IQEINAANSK225 QPIHMVYVPS235 HLYHMLFELF245 KNAMRATVES255 HESSLILPPI 265 KVMVALGEED275 LSIKMSDRGG285 GVPLRKIERL295 FSYMYSTPLA316 GFGYGLPISR 326 LYAKYFQGDL336 QLFSMEGFGT346 DAVIYLKALS356 TDSVERLPVY366 NKSAWRHYQT 376
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .A:243 or .A:247 or .A:248 or .A:250 or .A:251 or .A:282 or .A:284 or .A:286 or .A:287 or .A:295 or .A:315 or .A:316 or .A:317 or .A:318 or .A:319 or .A:320 or .A:321 or .A:322 or .A:323 or .A:338 or .A:346; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU243
4.884
ASN247
2.989
ALA248
4.130
ARG250
3.231
ALA251
3.496
ASP282
2.790
GLY284
4.696
GLY286
4.540
VAL287
3.362
LEU295
2.997
LEU315
4.877
|
|||||
| Ligand Name: N-[4-(2-Chloro-5-Methylpyrimidin-4-Yl)phenyl]-2,4-Dihydroxy-N-(4-{[(Trifluoroacetyl)amino]methyl}benzyl)benzamide | Ligand Info | |||||
| Structure Description | VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and induces context- dependent cytostasis in cancer cells | PDB:4V26 | ||||
| Method | X-ray diffraction | Resolution | 2.49 Å | Mutation | No | [2] |
| PDB Sequence |
ASAPKYIEHF
15 SKFSPSPLSM25 KQFLDFGSNA36 CEKTSFTFLR46 QELPVRLANI56 MKEINLLPDR 66 VLSTPSVQLV76 QSWYVQSLLD86 IMEFLDKDPE96 DHRTLSQFTD106 ALVTIRNRHN 116 DVVPTMAQGV126 LEYKDTYGDD136 PVSNQNIQYF146 LDRFYLSRIS156 IRMLINQHTL 166 IFDPKHIGSI183 DPNCNVSEVV193 KDAYDMAKLL203 CDKYYMASPD213 LEIQEINAAN 223 SKQPIHMVYV233 PSHLYHMLFE243 LFKNAMRATV253 ESHESSLILP263 PIKVMVALGE 273 EDLSIKMSDR283 GGGVPLRKIE293 RLFSYMYSTA303 PPLAGFGYGL322 PISRLYAKYF 332 QGDLQLFSME342 GFGTDAVIYL352 KALSTDSVER362 LPVY
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7TJ or .7TJ2 or .7TJ3 or :37TJ;style chemicals stick;color identity;select .A:243 or .A:244 or .A:246 or .A:247 or .A:248 or .A:250 or .A:251 or .A:254 or .A:255 or .A:282 or .A:284 or .A:285 or .A:286 or .A:287 or .A:295 or .A:315 or .A:316 or .A:322 or .A:338 or .A:340 or .A:346 or .A:348; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU243
4.842
LEU244
3.768
LYS246
3.470
ASN247
3.255
ALA248
4.083
ARG250
2.865
ALA251
3.439
GLU254
3.676
SER255
3.886
ASP282
2.393
GLY284
3.128
|
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| Ligand Name: N-(2-Aminoethyl)-2-{3-chloro-4-[(4-isopropylbenzyl)oxy]phenyl} acetamide | Ligand Info | |||||
| Structure Description | Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase | PDB:5M4P | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [3] |
| PDB Sequence |
GSAPKYIEHF
15 SKFSPSPLSM25 KQFLDFGSNA36 CEKTSFTFLR46 QELPVRLANI56 MKEINLLPDR 66 VLSTPSVQLV76 QSWYVQSLLD86 IMEFLDKDPE96 DHRTLSQFTD106 ALVTIRNRHN 116 DVVPTMAQGV126 LEYKDTYGDD136 PVSNQNIQYF146 LDRFYLSRIS156 IRMLINQHTL 166 IFDPKHIGSI183 DPNCNVSEVV193 KDAYDMAKLL203 CDKYYMASPD213 LEIQEINAAN 223 SKQPIHMVYV233 PSHLYHMLFE243 LFKNAMRATV253 ESHESSLILP263 PIKVMVALGE 273 EDLSIKMSDR283 GGGVPLRKIE293 RLFSYMYSTA303 PLAGFGYGLP323 ISRLYAKYFQ 333 GDLQLFSMEG343 FGTDAVIYLK353 ALSTDSVERL363 PVY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TF3 or .TF32 or .TF33 or :3TF3;style chemicals stick;color identity;select .A:63 or .A:64 or .A:66 or .A:67 or .A:73 or .A:122 or .A:125 or .A:126 or .A:129 or .A:138 or .A:139 or .A:142 or .A:143 or .A:146 or .A:147; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: N-[4-(2-chloro-5-methylpyrimidin-4-yl)phenyl]-2,4-dihydroxy-N-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]benzamide | Ligand Info | |||||
| Structure Description | Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase | PDB:5M4P | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [3] |
| PDB Sequence |
GSAPKYIEHF
15 SKFSPSPLSM25 KQFLDFGSNA36 CEKTSFTFLR46 QELPVRLANI56 MKEINLLPDR 66 VLSTPSVQLV76 QSWYVQSLLD86 IMEFLDKDPE96 DHRTLSQFTD106 ALVTIRNRHN 116 DVVPTMAQGV126 LEYKDTYGDD136 PVSNQNIQYF146 LDRFYLSRIS156 IRMLINQHTL 166 IFDPKHIGSI183 DPNCNVSEVV193 KDAYDMAKLL203 CDKYYMASPD213 LEIQEINAAN 223 SKQPIHMVYV233 PSHLYHMLFE243 LFKNAMRATV253 ESHESSLILP263 PIKVMVALGE 273 EDLSIKMSDR283 GGGVPLRKIE293 RLFSYMYSTA303 PLAGFGYGLP323 ISRLYAKYFQ 333 GDLQLFSMEG343 FGTDAVIYLK353 ALSTDSVERL363 PVY
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7FE or .7FE2 or .7FE3 or :37FE;style chemicals stick;color identity;select .A:243 or .A:244 or .A:246 or .A:247 or .A:248 or .A:250 or .A:251 or .A:254 or .A:255 or .A:282 or .A:284 or .A:285 or .A:286 or .A:287 or .A:295 or .A:315 or .A:316 or .A:322 or .A:338 or .A:340 or .A:346 or .A:348; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLU243
4.433
LEU244
3.656
LYS246
3.449
ASN247
3.186
ALA248
4.039
ARG250
3.004
ALA251
3.539
GLU254
3.808
SER255
4.017
ASP282
2.541
GLY284
3.190
|
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| Ligand Name: N-benzyl-2,4-dihydroxy-N-[4-[methyl(quinoxalin-6-ylmethyl)carbamoyl]phenyl]benzamide | Ligand Info | |||||
| Structure Description | Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase | PDB:5M4M | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [3] |
| PDB Sequence |
GSAPKYIEHF
15 SKFSPSPLSM25 KQFLDFGSNA36 CEKTSFTFLR46 QELPVRLANI56 MKEINLLPDR 66 VLSTPSVQLV76 QSWYVQSLLD86 IMEFLDKDPE96 DHRTLSQFTD106 ALVTIRNRHN 116 DVVPTMAQGV126 LEYKDTYGDD136 PVSNQNIQYF146 LDRFYLSRIS156 IRMLINQHTL 166 IFDPKHIGSI183 DPNCNVSEVV193 KDAYDMAKLL203 CDKYYMASPD213 LEIQEINAAN 223 SKQPIHMVYV233 PSHLYHMLFE243 LFKNAMRATV253 ESHESSLILP263 PIKVMVALGE 273 EDLSIKMSDR283 GGGVPLRKIE293 RLFSYMYSTA303 PPLAGFGYGL322 PISRLYAKYF 332 QGDLQLFSME342 GFGTDAVIYL352 KALSTDSVER362 LPVY
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7FW or .7FW2 or .7FW3 or :37FW;style chemicals stick;color identity;select .A:244 or .A:247 or .A:248 or .A:250 or .A:251 or .A:254 or .A:255 or .A:282 or .A:284 or .A:286 or .A:287 or .A:295 or .A:300 or .A:301 or .A:302 or .A:316 or .A:317 or .A:318 or .A:319 or .A:320 or .A:322 or .A:338 or .A:340 or .A:346 or .A:348; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU244
3.593
ASN247
3.423
ALA248
4.051
ARG250
2.479
ALA251
3.342
GLU254
4.041
SER255
4.515
ASP282
2.782
GLY284
3.551
GLY286
3.603
VAL287
3.119
LEU295
3.390
TYR300
3.595
|
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| Ligand Name: N-[2-(ethylamino)-2-oxoethyl]-2,4-dihydroxy-N-(4-methoxyphenyl)benzamide | Ligand Info | |||||
| Structure Description | Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase | PDB:5M4K | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [3] |
| PDB Sequence |
GSAPKYIEHF
15 SKFSPSPLSM25 KQFLDFNACE38 KTSFTFLRQE48 LPVRLANIMK58 EINLLPDRVL 68 STPSVQLVQS78 WYVQSLLDIM88 EFLDKDPEDH98 RTLSQFTDAL108 VTIRNRHNDV 118 VPTMAQGVLE128 YKDTYGDDPV138 SNQNIQYFLD148 RFYLSRISIR158 MLINQHTLIF 168 DPKHIGSIDP185 NCNVSEVVKD195 AYDMAKLLCD205 KYYMASPDLE215 IQEINAANSK 225 QPIHMVYVPS235 HLYHMLFELF245 KNAMRATVES255 HESSLILPPI265 KVMVALGEED 275 LSIKMSDRGG285 GVPLRKIERL295 FSYMYSTAPY320 GLPISRLYAK330 YFQGDLQLFS 340 MEGFGTDAVI350 YLKALSTDSV360 ERLPVY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7F9 or .7F92 or .7F93 or :37F9;style chemicals stick;color identity;select .A:244 or .A:247 or .A:248 or .A:250 or .A:251 or .A:254 or .A:255 or .A:282 or .A:284 or .A:286 or .A:287 or .A:295 or .A:322 or .A:338 or .A:340 or .A:346 or .A:348; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-[4-(2-Chloro-5-Methylpyrimidin-4-Yl)phenyl]-N-(4-{[(Difluoroacetyl)amino]methyl}benzyl)-2,4-Dihydroxybenzamide | Ligand Info | |||||
| Structure Description | VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and induces context- dependent cytostasis in cancer cells | PDB:4V25 | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [2] |
| PDB Sequence |
GSAPKYIEHF
15 SKFSPSPLSM25 KQFLDFGSAC37 EKTSFTFLRQ47 ELPVRLANIM57 KEINLLPDRV 67 LSTPSVQLVQ77 SWYVQSLLDI87 MEFLDKDPED97 HRTLSQFTDA107 LVTIRNRHND 117 VVPTMAQGVL127 EYKDTYGDDP137 VSNQNIQYFL147 DRFYLSRISI157 RMLINQHTLI 167 FDPKHIGSID184 PNCNVSEVVK194 DAYDMAKLLC204 DKYYMASPDL214 EIQEINAANS 224 KQPIHMVYVP234 SHLYHMLFEL244 FKNAMRATVE254 SHESSLILPP264 IKVMVALGEE 274 DLSIKMSDRG284 GGVPLRKIER294 LFSYMYSTAP304 PLAGFGYGLP323 ISRLYAKYFQ 333 GDLQLFSMEG343 FGTDAVIYLK353 ALSTDSVERL363 PVY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SZ6 or .SZ62 or .SZ63 or :3SZ6;style chemicals stick;color identity;select .A:243 or .A:244 or .A:246 or .A:247 or .A:248 or .A:250 or .A:251 or .A:254 or .A:255 or .A:282 or .A:284 or .A:285 or .A:286 or .A:287 or .A:295 or .A:315 or .A:316 or .A:322 or .A:338 or .A:340 or .A:346 or .A:348; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLU243
4.829
LEU244
3.891
LYS246
3.490
ASN247
2.916
ALA248
4.130
ARG250
3.410
ALA251
3.202
GLU254
3.448
SER255
3.856
ASP282
2.766
GLY284
3.008
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| Ligand Name: [2,4-Bis(Oxidanyl)phenyl]-[(2~{s})-2-Methyl-6-(3-Methylquinolin-2-Yl)-3,4-Dihydro-2~{h}-Quinolin-1-Yl]methanone | Ligand Info | |||||
| Structure Description | Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase | PDB:5M4N | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [3] |
| PDB Sequence |
GSAPKYIEHF
15 SKFSPSPLSM25 KQFLDFGACE38 KTSFTFLRQE48 LPVRLANIMK58 EINLLPDRVL 68 STPSVQLVQS78 WYVQSLLDIM88 EFLDKDPEDH98 RTLSQFTDAL108 VTIRNRHNDV 118 VPTMAQGVLE128 YKDTYGDDPV138 SNQNIQYFLD148 RFYLSRISIR158 MLINQHTLIF 168 DPKHIGSIDP185 NCNVSEVVKD195 AYDMAKLLCD205 KYYMASPDLE215 IQEINAANSK 225 QPIHMVYVPS235 HLYHMLFELF245 KNAMRATVES255 HESSLILPPI265 KVMVALGEED 275 LSIKMSDRGG285 GVPLRKIERL295 FSYMYSTAPY320 GLPISRLYAK330 YFQGDLQLFS 340 MEGFGTDAVI350 YLKALSTDSV360 ERLPVY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7FV or .7FV2 or .7FV3 or :37FV;style chemicals stick;color identity;select .A:243 or .A:244 or .A:247 or .A:248 or .A:250 or .A:251 or .A:282 or .A:284 or .A:286 or .A:287 or .A:295 or .A:322 or .A:338 or .A:340 or .A:346 or .A:348; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-[[[5-[5-Chloranyl-2,4-bis(oxidanyl)phenyl]-4-[4-(1-methylsulfonylpiperidin-4-yl)oxyphenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]cyclohexane-1-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of human PDK2 complexed with GM67520 | PDB:6LIO | ||||
| Method | X-ray diffraction | Resolution | 1.76 Å | Mutation | No | [4] |
| PDB Sequence |
AGAPKYIEHF
23 SKFSPSPLSM33 KQFLDFGSSN43 ACEKTSFTFL53 RQELPVRLAN63 IMKEINLLPD 73 RVLSTPSVQL83 VQSWYVQSLL93 DIMEFLDKDP103 EDHRTLSQFT113 DALVTIRNRH 123 NDVVPTMAQG133 VLEYKDTYGD143 DPVSNQNIQY153 FLDRFYLSRI163 SIRMLINQHT 173 LIFDGSTNPA183 HPKHIGSIDP193 NCNVSEVVKD203 AYDMAKLLCD213 KYYMASPDLE 223 IQEINAANSK233 QPIHMVYVPS243 HLYHMLFELF253 KNAMRATVES263 HESSLILPPI 273 KVMVALGEED283 LSIKMSDRGG293 GVPLRKIERL303 FSYMYSGFGY328 GLPISRLYAK 338 YFQGDLQLFS348 MEGFGTDAVI358 YLKALSTDSV368 ERLPVYNKSA378 WRHY |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EH3 or .EH32 or .EH33 or :3EH3;style chemicals stick;color identity;select .A:251 or .A:252 or .A:255 or .A:256 or .A:258 or .A:259 or .A:262 or .A:290 or .A:292 or .A:293 or .A:294 or .A:295 or .A:296 or .A:299 or .A:302 or .A:303 or .A:305 or .A:307 or .A:308 or .A:325 or .A:326 or .A:327 or .A:328 or .A:329 or .A:330 or .A:331 or .A:346 or .A:348 or .A:354 or .A:356; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLU251
3.882
LEU252
3.442
ASN255
3.480
ALA256
3.763
ARG258
3.069
ALA259
3.489
GLU262
4.569
ASP290
2.532
GLY292
3.956
GLY293
4.482
GLY294
3.246
VAL295
3.459
PRO296
4.324
LYS299
3.197
ARG302
3.680
|
|||||
| Ligand Name: Pdk4-IN-1 | Ligand Info | |||||
| Structure Description | Crystal structure of human PDK2 complexed with an allosteric inhibitor compound 8c | PDB:6LIL | ||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | No | [4] |
| PDB Sequence |
GAPKYIEHFS
24 KFSPSPLSMK34 QFLDFGSSNA44 CEKTSFTFLR54 QELPVRLANI64 MKEINLLPDR 74 VLSTPSVQLV84 QSWYVQSLLD94 IMEFLDKDPE104 DHRTLSQFTD114 ALVTIRNRHN 124 DVVPTMAQGV134 LEYKDTYGDD144 PVSNQNIQYF154 LDRFYLSRIS164 IRMLINQHTL 174 IFDGHPKHIG189 SIDPNCNVSE199 VVKDAYDMAK209 LLCDKYYMAS219 PDLEIQEINA 229 ANSKQPIHMV239 YVPSHLYHML249 FELFKNAMRA259 TVESHESSLI269 LPPIKVMVAL 279 GEEDLSIKMS289 DRGGGVPLRK299 IERLFSYMYS309 TAGTPLAGFG327 YGLPISRLYA 337 KYFQGDLQLF347 SMEGFGTDAV357 IYLKALSTDS367 VERLPV
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EGX or .EGX2 or .EGX3 or :3EGX;style chemicals stick;color identity;select .A:29 or .A:31 or .A:35 or .A:36 or .A:39 or .A:48 or .A:49 or .A:52; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4-[[[4-[3,5-Bis(fluoranyl)-4-(4-oxidanyl-4-oxidanylidene-butoxy)phenyl]-5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]benzoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of human PDK2 complexed with GM10030 | PDB:6LIN | ||||
| Method | X-ray diffraction | Resolution | 2.67 Å | Mutation | No | [4] |
| PDB Sequence |
DKALLKNASL
13 AGAPKYIEHF23 SKFSPSPLSM33 KQFLDFGSSN43 ACEKTSFTFL53 RQELPVRLAN 63 IMKEINLLPD73 RVLSTPSVQL83 VQSWYVQSLL93 DIMEFLDKDP103 EDHRTLSQFT 113 DALVTIRNRH123 NDVVPTMAQG133 VLEYKDTYGD143 DPVSNQNIQY153 FLDRFYLSRI 163 SIRMLINQHT173 LIFDGSTNPA183 HPKHIGSIDP193 NCNVSEVVKD203 AYDMAKLLCD 213 KYYMASPDLE223 IQEINAANSK233 QPIHMVYVPS243 HLYHMLFELF253 KNAMRATVES 263 HESSLILPPI273 KVMVALGEED283 LSIKMSDRGG293 GVPLRKIERL303 FSYMYFGYGL 330 PISRLYAKYF340 QGDLQLFSME350 GFGTDAVIYL360 KALSTDSVER370 LPVYNKSAWR 380 HYQTI
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EH0 or .EH02 or .EH03 or :3EH0;style chemicals stick;color identity;select .A:252 or .A:254 or .A:255 or .A:256 or .A:258 or .A:259 or .A:290 or .A:292 or .A:293 or .A:294 or .A:295 or .A:296 or .A:299 or .A:302 or .A:303 or .A:305 or .A:308 or .A:327 or .A:330 or .A:346 or .A:348 or .A:350 or .A:354 or .A:356; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU252
3.577
LYS254
4.773
ASN255
3.226
ALA256
3.787
ARG258
2.992
ALA259
3.478
ASP290
2.675
GLY292
3.561
GLY293
4.471
GLY294
3.437
VAL295
3.525
PRO296
3.815
|
|||||
| Ligand Name: 4-({5-[(Piperidin-4-Yl)amino]-1,3-Dihydro-2h-Isoindol-2-Yl}sulfonyl)benzene-1,3-Diol | Ligand Info | |||||
| Structure Description | Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PS35 | PDB:5J71 | ||||
| Method | X-ray diffraction | Resolution | 1.65 Å | Mutation | No | [5] |
| PDB Sequence |
SLAGAPKYIE
21 HFSKFSPSPL31 SMKQFLDCEK47 TSFTFLRQEL57 PVRLANIMKE67 INLLPDRVLS 77 TPSVQLVQSW87 YVQSLLDIME97 FLDKDPEDHR107 TLSQFTDALV117 TIRNRHNDVV 127 PTMAQGVLEY137 KDTYGDDPVS147 NQNIQYFLDR157 FYLSRISIRM167 LINQHTLIFH 187 IGSIDPNCNV197 SEVVKDAYDM207 AKLLCDKYYM217 ASPDLEIQEI227 NAANSQPIHM 238 VYVPSHLYHM248 LFELFKNAMR258 ATVESHESSL268 ILPPIKVMVA278 LGEEDLSIKM 288 SDRGGGVPLR298 KIERLFSYMG327 YGLPISRLYA337 KYFQGDLQLF347 SMEGFGTDAV 357 IYLKALSTDS367 VERLPVYNKS377 AWRHYDWC
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .P35 or .P352 or .P353 or :3P35;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:258 or .A:259 or .A:262 or .A:263 or .A:290 or .A:292 or .A:293 or .A:294 or .A:295 or .A:303 or .A:330 or .A:346 or .A:348 or .A:354 or .A:356; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 4-(Isoindolin-2-Ylsulfonyl)benzene-1,3-Diol | Ligand Info | |||||
| Structure Description | Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PS2 | PDB:4MPC | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [6] |
| PDB Sequence |
SLAGAPKYIE
21 HFSKFSPSPL31 SMKQFLDFGS41 SNACEKTSFT51 FLRQELPVRL61 ANIMKEINLL 71 PDRVLSTPSV81 QLVQSWYVQS91 LLDIMEFLDK101 DPEDHRTLSQ111 FTDALVTIRN 121 RHNDVVPTMA131 QGVLEYKDTY141 GDDPVSNQNI151 QYFLDRFYLS161 RISIRMLINQ 171 HTLIFDPAHP185 KHIGSIDPNC195 NVSEVVKDAY205 DMAKLLCDKY215 YMASPDLEIQ 225 EINAANSKQP235 IHMVYVPSHL245 YHMLFELFKN255 AMRATVESHE265 SSLILPPIKV 275 MVALGEEDLS285 IKMSDRGGGV295 PLRKIERLFS305 YMYSTGYGLP331 ISRLYAKYFQ 341 GDLQLFSMEG351 FGTDAVIYLK361 ALSTDSVERL371 PVYNKSAWRH381 YQTIQEAGDW 391 CVP
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PV2 or .PV22 or .PV23 or :3PV2;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:258 or .A:259 or .A:262 or .A:290 or .A:292 or .A:294 or .A:295 or .A:303 or .A:330 or .A:346 or .A:348 or .A:354 or .A:356; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (5-Bromo-2,4-Dihydroxyphenyl)(1,3-Dihydro-2h-Isoindol-2-Yl)methanone | Ligand Info | |||||
| Structure Description | Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PA1 | PDB:4MP2 | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [6] |
| PDB Sequence |
SLAGAPKYIE
21 HFSKFSPSPL31 SMKQFLDFGS41 SNACEKTSFT51 FLRQELPVRL61 ANIMKEINLL 71 PDRVLSTPSV81 QLVQSWYVQS91 LLDIMEFLDK101 DPEDHRTLSQ111 FTDALVTIRN 121 RHNDVVPTMA131 QGVLEYKDTY141 GDDPVSNQNI151 QYFLDRFYLS161 RISIRMLINQ 171 HTLIFDPAHP185 KHIGSIDPNC195 NVSEVVKDAY205 DMAKLLCDKY215 YMASPDLEIQ 225 EINAANSKQP235 IHMVYVPSHL245 YHMLFELFKN255 AMRATVESHE265 SSLILPPIKV 275 MVALGEEDLS285 IKMSDRGGGV295 PLRKIERLFS305 YMYSGYGLPI332 SRLYAKYFQG 342 DLQLFSMEGF352 GTDAVIYLKA362 LSTDSVERLP372 VYNKSAWRHY382 QTIQEAGDWC 392
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PV1 or .PV12 or .PV13 or :3PV1;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:258 or .A:259 or .A:262 or .A:290 or .A:292 or .A:294 or .A:295 or .A:303 or .A:330 or .A:346 or .A:348 or .A:354 or .A:356; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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||||||
| Ligand Name: 2-[(2,4-Dihydroxyphenyl)sulfonyl]-2,3-Dihydro-1h-Isoindole-4,6-Diol | Ligand Info | |||||
| Structure Description | Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PS10 | PDB:4MPN | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [6] |
| PDB Sequence |
SLAGAPKYIE
21 HFSKFSPSPL31 SMKQFLDFGS41 SNACEKTSFT51 FLRQELPVRL61 ANIMKEINLL 71 PDRVLSTPSV81 QLVQSWYVQS91 LLDIMEFLDK101 DPEDHRTLSQ111 FTDALVTIRN 121 RHNDVVPTMA131 QGVLEYKDTY141 GDDPVSNQNI151 QYFLDRFYLS161 RISIRMLINQ 171 HTLIFDPAHP185 KHIGSIDPNC195 NVSEVVKDAY205 DMAKLLCDKY215 YMASPDLEIQ 225 EINAANSKQP235 IHMVYVPSHL245 YHMLFELFKN255 AMRATVESHE265 SSLILPPIKV 275 MVALGEEDLS285 IKMSDRGGGV295 PLRKIERLFS305 YMYSTGYGLP331 ISRLYAKYFQ 341 GDLQLFSMEG351 FGTDAVIYLK361 ALSTDSVERL371 PVYNKSAWRH381 YQTIQEAGDW 391 CVP
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PV0 or .PV02 or .PV03 or :3PV0;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:258 or .A:259 or .A:262 or .A:263 or .A:290 or .A:292 or .A:294 or .A:295 or .A:303 or .A:330 or .A:346 or .A:348 or .A:354 or .A:356; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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||||||
| Ligand Name: 4-(1,3-Dihydro-2h-Isoindol-2-Ylcarbonyl)benzene-1,3-Diol | Ligand Info | |||||
| Structure Description | Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PA7 | PDB:4MP7 | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [6] |
| PDB Sequence |
SLAGAPKYIE
21 HFSKFSPSPL31 SMKQFLDFGS41 SNACEKTSFT51 FLRQELPVRL61 ANIMKEINLL 71 PDRVLSTPSV81 QLVQSWYVQS91 LLDIMEFLDK101 DPEDHRTLSQ111 FTDALVTIRN 121 RHNDVVPTMA131 QGVLEYKDTY141 GDDPVSNQNI151 QYFLDRFYLS161 RISIRMLINQ 171 HTLIFDPAHP185 KHIGSIDPNC195 NVSEVVKDAY205 DMAKLLCDKY215 YMASPDLEIQ 225 EINAANSKQP235 IHMVYVPSHL245 YHMLFELFKN255 AMRATVESHE265 SSLILPPIKV 275 MVALGEEDLS285 IKMSDRGGGV295 PLRKIERLFS305 YMYSTGYGLP331 ISRLYAKYFQ 341 GDLQLFSMEG351 FGTDAVIYLK361 ALSTDSVERL371 PVYNKSAWRH381 YQTIQEAGDW 391 CVP
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PFT or .PFT2 or .PFT3 or :3PFT;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:258 or .A:259 or .A:262 or .A:290 or .A:292 or .A:294 or .A:295 or .A:303 or .A:330 or .A:346 or .A:348 or .A:354 or .A:356; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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||||||
| Ligand Name: 4-[(5-Hydroxy-1,3-Dihydro-2h-Isoindol-2-Yl)sulfonyl]benzene-1,3-Diol | Ligand Info | |||||
| Structure Description | Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PS8 | PDB:4MPE | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [6] |
| PDB Sequence |
SLAGAPKYIE
21 HFSKFSPSPL31 SMKQFLDFGS41 SNACEKTSFT51 FLRQELPVRL61 ANIMKEINLL 71 PDRVLSTPSV81 QLVQSWYVQS91 LLDIMEFLDK101 DPEDHRTLSQ111 FTDALVTIRN 121 RHNDVVPTMA131 QGVLEYKDTY141 GDDPVSNQNI151 QYFLDRFYLS161 RISIRMLINQ 171 HTLIFDPAHP185 KHIGSIDPNC195 NVSEVVKDAY205 DMAKLLCDKY215 YMASPDLEIQ 225 EINAANSKQP235 IHMVYVPSHL245 YHMLFELFKN255 AMRATVESHE265 SSLILPPIKV 275 MVALGEEDLS285 IKMSDRGGGV295 PLRKIERLFS305 YMYSTGYGLP331 ISRLYAKYFQ 341 GDLQLFSMEG351 FGTDAVIYLK361 ALSTDSVERL371 PVYNKSAWRH381 YQTIQEAGDW 391 CVP
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PV8 or .PV82 or .PV83 or :3PV8;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:258 or .A:259 or .A:262 or .A:263 or .A:290 or .A:292 or .A:294 or .A:295 or .A:303 or .A:330 or .A:346 or .A:348 or .A:354 or .A:356; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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||||||
| Ligand Name: (3s)-3-Amino-4-[4-({2-[(2,4-Dihydroxyphenyl)sulfonyl]-2h-Isoindol-5-Yl}amino)piperidin-1-Yl]-4-Oxobutanamide | Ligand Info | |||||
| Structure Description | Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PS46 | PDB:5J6A | ||||
| Method | X-ray diffraction | Resolution | 2.04 Å | Mutation | No | [5] |
| PDB Sequence |
ASLAGAPKYI
20 EHFSKFSPSP30 LSMKQFLDFG40 SCEKTSFTFL53 RQELPVRLAN63 IMKEINLLPD 73 RVLSTPSVQL83 VQSWYVQSLL93 DIMEFLDKDP103 EDHRTLSQFT113 DALVTIRNRH 123 NDVVPTMAQG133 VLEYKDTYGD143 DPVSNQNIQY153 FLDRFYLSRI163 SIRMLINQHT 173 LIFDHIGSID192 PNCNVSEVVK202 DAYDMAKLLC212 DKYYMASPDL222 EIQEINAANS 232 KQPIHMVYVP242 SHLYHMLFEL252 FKNAMRATVE262 SHESSLILPP272 IKVMVALGEE 282 DLSIKMSDRG292 GGVPLRKIER302 LFSYMYSTGF326 GYGLPISRLY336 AKYFQGDLQL 346 FSMEGFGTDA356 VIYLKALSTD366 SVERLPV
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .P46 or .P462 or .P463 or :3P46;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:258 or .A:259 or .A:262 or .A:263 or .A:265 or .A:290 or .A:292 or .A:294 or .A:295 or .A:303 or .A:330 or .A:346 or .A:348 or .A:354 or .A:356; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-cyclopropyl-2-methyl-9H-pyrido[2,3-b]indole | Ligand Info | |||||
| Structure Description | Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 5 | PDB:7VBU | ||||
| Method | X-ray diffraction | Resolution | 1.89 Å | Mutation | No | [7] |
| PDB Sequence |
GSAPKYIEHF
23 SKFSPSPLSM33 KQFLDFGSSN43 ACEKTSFTFL53 RQELPVRLAN63 IMKEINLLPD 73 RVLSTPSVQL83 VQSWYVQSLL93 DIMEFLDKDP103 EDHRTLSQFT113 DALVTIRNRH 123 NDVVPTMAQG133 VLEYKDTYGD143 DPVSNQNIQY153 FLDRFYLSRI163 SIRMLINQHT 173 LIFDGKHIGS190 IDPNCNVSEV200 VKDAYDMAKL210 LCDKYYMASP220 DLEIQEINAA 230 NSKQPIHMVY240 VPSHLYHMLF250 ELFKNAMRAT260 VESHESSLIL270 PPIKVMVALG 280 EEDLSIKMSD290 RGGGVPLRKI300 ERLFSYMYST310 APGYGLPISR334 LYAKYFQGDL 344 QLFSMEGFGT354 DAVIYLKALS364 TDSVERLPVY374
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6I4 or .6I42 or .6I43 or :36I4;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:259 or .A:288 or .A:290 or .A:292 or .A:294 or .A:295 or .A:303 or .A:330 or .A:346 or .A:354 or .A:355 or .A:356; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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||||||
| Ligand Name: 5-bromanyl-2-methyl-6-propyl-7H-pyrrolo[2,3-d]pyrimidine | Ligand Info | |||||
| Structure Description | Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 13 | PDB:7EBH | ||||
| Method | X-ray diffraction | Resolution | 1.96 Å | Mutation | No | [8] |
| PDB Sequence |
GSAPKYIEHF
23 SKFSPSPLSM33 KQFLDFGSSN43 ACEKTSFTFL53 RQELPVRLAN63 IMKEINLLPD 73 RVLSTPSVQL83 VQSWYVQSLL93 DIMEFLDKDP103 EDHRTLSQFT113 DALVTIRNRH 123 NDVVPTMAQG133 VLEYKDTYGD143 DPVSNQNIQY153 FLDRFYLSRI163 SIRMLINQHT 173 LIFDGPKHIG189 SIDPNCNVSE199 VVKDAYDMAK209 LLCDKYYMAS219 PDLEIQEINA 229 ANSKQPIHMV239 YVPSHLYHML249 FELFKNAMRA259 TVESHESSLI269 LPPIKVMVAL 279 GEEDLSIKMS289 DRGGGVPLRK299 IERLFSYMYS309 TAPGYGLPIS333 RLYAKYFQGD 343 LQLFSMEGFG353 TDAVIYLKAL363 STDSVERLPV373 Y
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .J0F or .J0F2 or .J0F3 or :3J0F;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:259 or .A:288 or .A:289 or .A:290 or .A:292 or .A:294 or .A:295 or .A:303 or .A:330 or .A:346 or .A:354 or .A:355 or .A:356; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 1H-Pyrrolo[2,3-B]pyridine-3-carbonitrile | Ligand Info | |||||
| Structure Description | Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 2 | PDB:7EAS | ||||
| Method | X-ray diffraction | Resolution | 1.97 Å | Mutation | No | [8] |
| PDB Sequence |
GSAPKYIEHF
23 SKFSPSPLSM33 KQFLDFGSSN43 ACEKTSFTFL53 RQELPVRLAN63 IMKEINLLPD 73 RVLSTPSVQL83 VQSWYVQSLL93 DIMEFLDKDP103 EDHRTLSQFT113 DALVTIRNRH 123 NDVVPTMAQG133 VLEYKDTYGD143 DPVSNQNIQY153 FLDRFYLSRI163 SIRMLINQHT 173 LIFDGPKHIG189 SIDPNCNVSE199 VVKDAYDMAK209 LLCDKYYMAS219 PDLEIQEINA 229 ANSKQPIHMV239 YVPSHLYHML249 FELFKNAMRA259 TVESHESSLI269 LPPIKVMVAL 279 GEEDLSIKMS289 DRGGGVPLRK299 IERLFSYMYS309 TAPGYGLPIS333 RLYAKYFQGD 343 LQLFSMEGFG353 TDAVIYLKAL363 STDSVERLPV373 Y
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .42A or .42A2 or .42A3 or :342A;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:259 or .A:290 or .A:294 or .A:295 or .A:303 or .A:330 or .A:346 or .A:354 or .A:356; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: methyl 8-cyclopropyl-2-methyl-9H-pyrido[2,3-b]indole-3-carboxylate | Ligand Info | |||||
| Structure Description | Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 7 | PDB:7VBV | ||||
| Method | X-ray diffraction | Resolution | 2.21 Å | Mutation | No | [7] |
| PDB Sequence |
GSAPKYIEHF
23 SKFSPSPLSM33 KQFLDFGSSN43 ACEKTSFTFL53 RQELPVRLAN63 IMKEINLLPD 73 RVLSTPSVQL83 VQSWYVQSLL93 DIMEFLDKDP103 EDHRTLSQFT113 DALVTIRNRH 123 NDVVPTMAQG133 VLEYKDTYGD143 DPVSNQNIQY153 FLDRFYLSRI163 SIRMLINQHT 173 LIFDGKHIGS190 IDPNCNVSEV200 VKDAYDMAKL210 LCDKYYMASP220 DLEIQEINAA 230 NSKQPIHMVY240 VPSHLYHMLF250 ELFKNAMRAT260 VESHESSLIL270 PPIKVMVALG 280 EEDLSIKMSD290 RGGGVPLRKI300 ERLFSYMYSG327 YGLPISRLYA337 KYFQGDLQLF 347 SMEGFGTDAV357 IYLKALSTDS367 VERLPVY
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .67V or .67V2 or .67V3 or :367V;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:259 or .A:288 or .A:289 or .A:290 or .A:292 or .A:293 or .A:294 or .A:295 or .A:299 or .A:303 or .A:330 or .A:346 or .A:354 or .A:355 or .A:356; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Oxindole | Ligand Info | |||||
| Structure Description | Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 1 | PDB:7EA0 | ||||
| Method | X-ray diffraction | Resolution | 2.34 Å | Mutation | No | [8] |
| PDB Sequence |
GSAPKYIEHF
23 SKFSPSPLSM33 KQFLDFGSSN43 ACEKTSFTFL53 RQELPVRLAN63 IMKEINLLPD 73 RVLSTPSVQL83 VQSWYVQSLL93 DIMEFLDKDP103 EDHRTLSQFT113 DALVTIRNRH 123 NDVVPTMAQG133 VLEYKDTYGD143 DPVSNQNIQY153 FLDRFYLSRI163 SIRMLINQHT 173 LIFDGKHIGS190 IDPNCNVSEV200 VKDAYDMAKL210 LCDKYYMASP220 DLEIQEINAA 230 NSKQPIHMVY240 VPSHLYHMLF250 ELFKNAMRAT260 VESHESSLIL270 PPIKVMVALG 280 EEDLSIKMSD290 RGGGVPLRKI300 ERLFSYMYST310 APGYGLPISR334 LYAKYFQGDL 344 QLFSMEGFGT354 DAVIYLKALS364 TDSVERLPVY374
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .W6P or .W6P2 or .W6P3 or :3W6P;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:259 or .A:290 or .A:292 or .A:294 or .A:295 or .A:300 or .A:303 or .A:330 or .A:346 or .A:354 or .A:356; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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||||||
| Ligand Name: 4-({(2R,5S)-2,5-Dimethyl-4-[(2R)-3,3,3-trifluoro-2-hydroxy-2-methylpropanoyl]piperazin-1-YL}carbonyl)benzonitrile | Ligand Info | |||||
| Structure Description | crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands | PDB:2BU5 | ||||
| Method | X-ray diffraction | Resolution | 2.35 Å | Mutation | No | [1] |
| PDB Sequence |
GSAPKYIEHF
15 SKFSPSPLSM25 KQFLDFSNAC37 EKTSFTFLRQ47 ELPVRLANIM57 KEINLLPDRV 67 LSTPSVQLVQ77 SWYVQSLLDI87 MEFLDKDPED97 HRTLSQFTDA107 LVTIRNRHND 117 VVPTMAQGVL127 EYKDTYGDDP137 VSNQNIQYFL147 DRFYLSRISI157 RMLINQHTLI 167 FDKHIGSIDP185 NCNVSEVVKD195 AYDMAKLLCD205 KYYMASPDLE215 IQEINAANSK 225 QPIHMVYVPS235 HLYHMLFELF245 KNAMRATVES255 HESSLILPPI265 KVMVALGEED 275 LSIKMSDRGG285 GVPLRKIERL295 FSYMYSTAPG319 YGLPISRLYA329 KYFQGDLQLF 339 SMEGFGTDAV349 IYLKALSTDS359 VERLPVYNKS369 AWRHYQTIQE379 AGDWCV |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TF1 or .TF12 or .TF13 or :3TF1;style chemicals stick;color identity;select .A:21 or .A:23 or .A:27 or .A:28 or .A:31 or .A:40 or .A:41 or .A:44 or .A:45 or .A:159 or .A:160 or .A:161 or .A:163 or .A:164 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Dichloroacetic acid | Ligand Info | |||||
| Structure Description | crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands | PDB:2BU8 | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [1] |
| PDB Sequence |
GSAPKYIEHF
15 SKFSPSPLSM25 KQFLDFGSSN35 ACEKTSFTFL45 RQELPVRLAN55 IMKEINLLPD 65 RVLSTPSVQL75 VQSWYVQSLL85 DIMEFLDKDP95 EDHRTLSQFT105 DALVTIRNRH 115 NDVVPTMAQG125 VLEYKDTYGD135 DPVSNQNIQY145 FLDRFYLSRI155 SIRMLINQHT 165 LIFDGSTNPA175 HPKHIGSIDP185 NCNVSEVVKD195 AYDMAKLLCD205 KYYMASPDLE 215 IQEINAANSK225 QPIHMVYVPS235 HLYHMLFELF245 KNAMRATVES255 HESSLILPPI 265 KVMVALGEED275 LSIKMSDRGG285 GVPLRKIERL295 FSYMYSTPLA316 GFGYGLPISR 326 LYAKYFQGDL336 QLFSMEGFGT346 DAVIYLKALS356 TDSVERLPVY366 NKSAWRHYQT 376
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TF4 or .TF42 or .TF43 or :3TF4;style chemicals stick;color identity;select .A:53 or .A:80 or .A:83 or .A:111 or .A:112 or .A:115 or .A:154 or .A:157 or .A:158 or .A:161; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (3~{S})-3-[5-(8-cyclopropyl-2-methyl-9~{H}-pyrido[2,3-b]indol-3-yl)-1,3,4-oxadiazol-2-yl]-4-methyl-~{N}-[(1~{R})-1-phenylethyl]pentanamide | Ligand Info | |||||
| Structure Description | Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 20 | PDB:7VBX | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [7] |
| PDB Sequence |
GSAPKYIEHF
23 SKFSPSPLSM33 KQFLDFGSSN43 ACEKTSFTFL53 RQELPVRLAN63 IMKEINLLPD 73 RVLSTPSVQL83 VQSWYVQSLL93 DIMEFLDKDP103 EDHRTLSQFT113 DALVTIRNRH 123 NDVVPTMAQG133 VLEYKDTYGD143 DPVSNQNIQY153 FLDRFYLSRI163 SIRMLINQHT 173 LIFDGSPKHI188 GSIDPNCNVS198 EVVKDAYDMA208 KLLCDKYYMA218 SPDLEIQEIN 228 AANSKQPIHM238 VYVPSHLYHM248 LFELFKNAMR258 ATVESHESSL268 ILPPIKVMVA 278 LGEEDLSIKM288 SDRGGGVPLR298 KIERLFSYMY308 STAPGYGLPI332 SRLYAKYFQG 342 DLQLFSMEGF352 GTDAVIYLKA362 LSTDSVERLP372
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5ZP or .5ZP2 or .5ZP3 or :35ZP;style chemicals stick;color identity;select .A:252 or .A:255 or .A:256 or .A:258 or .A:259 or .A:262 or .A:288 or .A:290 or .A:292 or .A:294 or .A:295 or .A:296 or .A:299 or .A:302 or .A:303 or .A:330 or .A:346 or .A:354 or .A:355 or .A:356; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU252
3.720
ASN255
3.382
ALA256
3.774
ARG258
3.280
ALA259
3.303
GLU262
3.606
MET288
3.274
ASP290
2.932
GLY292
3.925
GLY294
3.630
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Regulatory roles of the N-terminal domain based on crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands. Biochemistry. 2006 Jan 17;45(2):402-15. | ||||
| REF 2 | VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and induces context-dependent cytostasis in cancer cells. Oncotarget. 2014 Dec 30;5(24):12862-76. | ||||
| REF 3 | Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase. J Med Chem. 2017 Mar 23;60(6):2271-2286. | ||||
| REF 4 | Structural basis for the inhibition of PDK2 by novel ATP- and lipoyl-binding site targeting compounds. Biochem Biophys Res Commun. 2020 Jun 30;527(3):778-784. | ||||
| REF 5 | Development of Dihydroxyphenyl Sulfonylisoindoline Derivatives as Liver-Targeting Pyruvate Dehydrogenase Kinase Inhibitors. J Med Chem. 2017 Feb 9;60(3):1142-1150. | ||||
| REF 6 | Structure-guided development of specific pyruvate dehydrogenase kinase inhibitors targeting the ATP-binding pocket. J Biol Chem. 2014 Feb 14;289(7):4432-43. | ||||
| REF 7 | Structure-based drug design of novel and highly potent pyruvate dehydrogenase kinase inhibitors.. doi:10.1016/j.bmc.2021.116514. | ||||
| REF 8 | Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases. Bioorg Med Chem. 2021 Aug 15;44:116283. | ||||
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