Target Binding Site Detail
Target General Information | Top | ||||
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Target ID | T32880 | Target Info | |||
Target Name | HIF-prolyl hydroxylase 2 (HPH-2) | ||||
Synonyms | SM-20; Prolyl hydroxylase domain-containing protein 2; PHD2; Hypoxia-inducible factor prolyl hydroxylase 2; HPH-2; HIF-PH2; Egl nine homolog 1; C1orf12 | ||||
Target Type | Patented-recorded Target | ||||
Gene Name | EGLN1 | ||||
Biochemical Class | Paired donor oxygen oxidoreductase | ||||
UniProt ID |
Ligand General Information | Top | ||||
---|---|---|---|---|---|
Ligand Name | FG-2216 | Ligand Info | |||
Canonical SMILES | C1=CC=C2C(=C1)C(=C(N=C2Cl)C(=O)NCC(=O)O)O | ||||
InChI | 1S/C12H9ClN2O4/c13-11-7-4-2-1-3-6(7)10(18)9(15-11)12(19)14-5-8(16)17/h1-4,18H,5H2,(H,14,19)(H,16,17) | ||||
InChIKey | OUQVKRKGTAUJQA-UHFFFAOYSA-N | ||||
PubChem Compound ID | 6914666 |
Drug Binding Sites of Target | Top | |||||
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PDB ID: 5LB6 HIF prolyl hydroxylase 2 (PHD2/EGLN1) R371H variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9) | ||||||
Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [1] |
PDB Sequence |
LPALKLALEY
197 IVPCMNKHGI207 CVVDDFLGKE217 TGQQIGDEVR227 ALHDTGKFTD237 GQLVSQKSDS 247 SKDIRGDKIT257 WIEGKEPGCE267 TIGLLMSSMD277 DLIRHCNGKL287 GSYKINGRTK 297 AMVACYPGNG307 TGYVRHVDNP317 NGDGRCVTCI327 YYLNKDWDAK337 VSGGILRIFP 347 EGKAQFADIE357 PKFDRLLFFW367 SDRHNPHEVQ377 PAYATRYAIT387 VWYFDADERA 397 RAKVKYLKGV410 R
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GLN239
4.714
ASP254
2.538
ILE256
2.360
MET299
2.781
ALA301
3.394
TYR303
1.781
TYR310
2.988
HIS313
2.868
ASP315
3.429
ARG322
4.728
ILE327
2.622
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PDB ID: 5LBB HIF prolyl hydroxylase 2 (PHD2/EGLN1) R396T variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9) | ||||||
Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [1] |
PDB Sequence |
NGQTLPALKL
193 ALEYIVPCMN203 KHGICVVDDF213 LGKETGQQIG223 DEVRALHDTG233 KFTDGQLVSQ 243 KSDSSKDIRG253 DKITWIEGKE263 PGCETIGLLM273 SSMDDLIRHC283 NGKLGSYKIN 293 GRTKAMVACY303 PGNGTGYVRH313 VDNPNGDGRC323 VTCIYYLNKD333 WDAKVSGGIL 343 RIFPEGKAQF353 ADIEPKFDRL363 LFFWSDRRNP373 HEVQPAYATR383 YAITVWYFDA 393 DETARAKVKY403 LTGGVRVEL
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ASP254
2.579
ILE256
2.322
MET299
2.838
ALA301
3.374
TYR303
1.734
TYR310
3.242
HIS313
2.842
ASP315
3.411
ARG322
4.700
ILE327
2.570
TYR329
1.827
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PDB ID: 4UWD HIF prolyl hydroxylase 2 (PHD2/ EGLN1) D315E VARIANT in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9) | ||||||
Method | X-ray diffraction | Resolution | 1.72 Å | Mutation | Yes | [2] |
PDB Sequence |
LPALKLALEY
197 IVPCMNKHGI207 CVVDDFLGKE217 TGQQIGDEVR227 ALHDTGKFTD237 GQLVSQKSDS 247 SKDIRGDKIT257 WIEGKEPGCE267 TIGLLMSSMD277 DLIRHCNGKL287 GSYKINGRTK 297 AMVACYPGNG307 TGYVRHVENP317 NGDGRCVTCI327 YYLNKDWDAK337 VSGGILRIFP 347 EGKAQFADIE357 PKFDRLLFFW367 SDRRNPHEVQ377 PAYATRYAIT387 VWYFDADERA 397 RAKVKYLGEK408 G
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ASP254
2.495
ILE256
2.344
MET299
2.874
ALA301
3.377
TYR303
1.897
TYR310
3.283
HIS313
2.696
GLU315
3.656
ARG322
4.697
ILE327
2.884
TYR329
1.788
|
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PDB ID: 5LBE HIF prolyl hydroxylase 2 (PHD2/EGLN1) G294E variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/FG2216) | ||||||
Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | Yes | [1] |
PDB Sequence |
LPALKLALEY
197 IVPCMNKHGI207 CVVDDFLGKE217 TGQQIGDEVR227 ALHDTGKFTD237 GQLVSQDSSK 249 DIRGDKITWI259 EGKEPGCETI269 GLLMSSMDDL279 IRHCNGKLGS289 YKINERTKAM 299 VACYPGNGTG309 YVRHVDNPNG319 DGRCVTCIYY329 LNKDWDAKVS339 GGILRIFPEG 349 KAQFADIEPK359 FDRLLFFWSD369 RRNPHEVQPA379 YATRYAITVW389 YFDADERARA 399 KVKYLGVRVE413
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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 .UN9 or .UN92 or .UN93 or :3UN9;style chemicals stick;color identity;select .A:254 or .A:256 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:322 or .A:327 or .A:329 or .A:343 or .A:358 or .A:366 or .A:374 or .A:375 or .A:376 or .A:383 or .A:385 or .A:389; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASP254
2.577
ILE256
2.245
MET299
2.843
ALA301
3.346
TYR303
1.765
TYR310
3.291
HIS313
2.856
ASP315
3.515
ARG322
4.690
ILE327
2.653
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PDB ID: 4BQX HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9) | ||||||
Method | X-ray diffraction | Resolution | 1.79 Å | Mutation | No | [3] |
PDB Sequence |
LPALKLALEY
197 IVPCMNKHGI207 CVVDDFLGKE217 TGQQIGDEVR227 ALHDTGKFTD237 GQLVSQKSDS 247 SKDIRGDKIT257 WIEGKEPGCE267 TIGLLMSSMD277 DLIRHCNGKL287 GSYKINGRTK 297 AMVACYPGNG307 TGYVRHVDNP317 NGDGRCVTCI327 YYLNKDWDAK337 VSGGILRIFP 347 EGKAQFADIE357 PKFDRLLFFW367 SDRRNPHEVQ377 PAYATRYAIT387 VWYFDADERA 397 RAKVKYL
|
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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 .UN9 or .UN92 or .UN93 or :3UN9;style chemicals stick;color identity;select .A:254 or .A:256 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:327 or .A:329 or .A:343 or .A:374 or .A:376 or .A:383 or .A:385 or .A:389; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 5LBC HIF prolyl hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/FG2216) | ||||||
Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | Yes | [1] |
PDB Sequence |
LPALKLALEY
197 IVPCMNKHGI207 CVVDDFLGKE217 TGQQIGDEVR227 ALHDTGKFTD237 GQLVSQKSDS 247 SKDIRGDKIT257 WIEGKEPGCE267 TIGLLMSSMD277 DLVLHCNGKL287 GSYKVNGRTK 297 AMVACYPGNG307 TGYVRHVDNP317 NGDGRCVTCI327 YYLNKDWDAK337 VSGGILRIFP 347 EGKAQFADIE357 PKFDRLLFFW367 SDRRNPHEVQ377 PAYATRYAIT387 VWYFDADERA 397 RAKVKYLVRV412 EL
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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 .UN9 or .UN92 or .UN93 or :3UN9;style chemicals stick;color identity;select .A:254 or .A:256 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:322 or .A:327 or .A:329 or .A:343 or .A:358 or .A:366 or .A:374 or .A:375 or .A:376 or .A:383 or .A:385 or .A:387 or .A:389; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASP254
2.601
ILE256
2.269
MET299
2.910
ALA301
3.348
TYR303
2.286
TYR310
3.073
HIS313
2.808
ASP315
3.376
ARG322
4.819
ILE327
2.540
TYR329
1.844
|
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PDB ID: 5LAT HIF prolyl hydroxylase 2 (PHD2/EGLN1) P317R variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9) | ||||||
Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | Yes | [1] |
PDB Sequence |
LPALKLALEY
197 IVPCMNKHGI207 CVVDDFLGKE217 TGQQIGDEVR227 ALHDTGKFTD237 GQLVSQKSDS 247 SKDIRGDKIT257 WIEGKEPGCE267 TIGLLMSSMD277 DLIRHCNGKL287 GSYKINGRTK 297 AMVACYPGNG307 TGYVRHVDNR317 NGDGRCVTCI327 YYLNKDWDAK337 VSGGILRIFP 347 EGKAQFADIE357 PKFDRLLFFW367 SDRRNPHEVQ377 PAYATRYAIT387 VWYFDADERA 397 RAKVKYLKGV410 R
|
|||||
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UN9 or .UN92 or .UN93 or :3UN9;style chemicals stick;color identity;select .A:254 or .A:256 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:322 or .A:327 or .A:329 or .A:343 or .A:358 or .A:366 or .A:374 or .A:375 or .A:376 or .A:383 or .A:385 or .A:389; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASP254
2.541
ILE256
2.309
MET299
2.710
ALA301
3.364
TYR303
1.632
TYR310
3.059
HIS313
2.813
ASP315
3.450
ARG322
4.745
ILE327
2.706
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PDB ID: 5LBF HIF prolyl hydroxylase 2 (PHD2/EGLN1) K293K/G294E variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/FG2216) | ||||||
Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | Yes | [1] |
PDB Sequence |
LPALKLALEY
197 IVPCMNKHGI207 CVVDDFLGKE217 TGQQIGDEVR227 ALHDTGKFTD237 GQLVSQKSDS 247 SKDIRGDKIT257 WIEGKEPGCE267 TIGLLMSSMD277 DLIRHCNGKL287 GSYKIKERTK 297 AMVACYPGNG307 TGYVRHVDNP317 NGDGRCVTCI327 YYLNKDWDAK337 VSGGILRIFP 347 EGKAQFADIE357 PKFDRLLFFW367 SDRRNPHEVQ377 PAYATRYAIT387 VWYFDADERA 397 RAKVKYLEKG409 VRVE
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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 .UN9 or .UN92 or .UN93 or :3UN9;style chemicals stick;color identity;select .A:254 or .A:256 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:322 or .A:327 or .A:329 or .A:343 or .A:358 or .A:364 or .A:366 or .A:374 or .A:375 or .A:376 or .A:383 or .A:385 or .A:389; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASP254
2.552
ILE256
2.322
MET299
2.742
ALA301
3.426
TYR303
1.716
TYR310
3.250
HIS313
2.847
ASP315
3.524
ARG322
4.631
ILE327
2.544
TYR329
1.843
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PDB ID: 2Y33 S-nitrosylated PHD2 (GSNO soaked) in complex with Zn(II) and UN9 | ||||||
Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [4] |
PDB Sequence |
LPALKLALEY
197 IVPCMNKHGI207 CVVDDFLGKE217 TGQQIGDEVR227 ALHDTGKFTD237 GQLVSQKSDS 247 SKDIRGDKIT257 WIEGKEPGCE267 TIGLLMSSMD277 DLIRHCNGKL287 GSYKINGRTK 297 AMVAYPGNGT308 GYVRHVDNPN318 GDGRCVTCIY328 YLNKDWDAKV338 SGGILRIFPE 348 GKAQFADIEP358 KFDRLLFFWS368 DRRNPHEVQP378 AYATRYAITV388 WYFDADERAR 398 AKVKY
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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 .UN9 or .UN92 or .UN93 or :3UN9;style chemicals stick;color identity;select .A:254 or .A:256 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:327 or .A:329 or .A:343 or .A:374 or .A:376 or .A:383 or .A:385 or .A:389; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 2Y34 S-nitrosylated PHD2 (NO exposed) in complex with Fe(II) and UN9 | ||||||
Method | X-ray diffraction | Resolution | 2.01 Å | Mutation | No | [4] |
PDB Sequence |
PLPALKLALE
196 YIVPCMNKHG206 ICVVDDFLGK216 ETGQQIGDEV226 RALHDTGKFT236 DGQLVSQKSD 246 SSKDIRGDKI256 TWIEGKEPGC266 ETIGLLMSSM276 DDLIRHCNGK286 LGSYKINGRT 296 KAMVAYPGNG307 TGYVRHVDNP317 NGDGRCVTCI327 YYLNKDWDAK337 VSGGILRIFP 347 EGKAQFADIE357 PKFDRLLFFW367 SDRRNPHEVQ377 PAYATRYAIT387 VWYFDADERA 397 RAKVK
|
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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 .UN9 or .UN92 or .UN93 or :3UN9;style chemicals stick;color identity;select .A:254 or .A:256 or .A:258 or .A:296 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:320 or .A:322 or .A:327 or .A:329 or .A:343 or .A:374 or .A:376 or .A:383 or .A:385 or .A:389 or .A:391 or .A:396; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASP254
3.063
ILE256
3.747
TRP258
3.344
THR296
3.779
MET299
3.453
ALA301
4.316
TYR303
2.600
TYR310
3.556
HIS313
3.064
ASP315
3.270
ASP320
3.231
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PDB ID: 2HBT Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor | ||||||
Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [5] |
PDB Sequence |
LPALKLALEY
197 IVPCMNKHGI207 CVVDDFLGKE217 TGQQIGDEVR227 ALHDTGKFTD237 GQLVSQKSDS 247 SKDIRGDKIT257 WIEGKEPGCE267 TIGLLMSSMD277 DLIRHCNGKL287 GSYKINGRTK 297 AMVACYPGNG307 TGYVRHVDNP317 NGDGRCVTCI327 YYLNKDWDAK337 VSGGILRIFP 347 EGKAQFADIE357 PKFDRLLFFW367 SDRRNPHEVQ377 PAYATRYAIT387 VWYFDADERA 397 RAKVKYLKGV410 RVEL
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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 .UN9 or .UN92 or .UN93 or :3UN9;style chemicals stick;color identity;select .A:254 or .A:256 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:327 or .A:329 or .A:343 or .A:374 or .A:376 or .A:383 or .A:385 or .A:389; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 2HBU Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor | ||||||
Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [6] |
PDB Sequence |
LPALKLALEY
197 IVPCMNKHGI207 CVVDDFLGKE217 TGQQIGDEVR227 ALHDTGKFTD237 GQLVSQKSDS 247 SKDIRGDKIT257 WIEGKEPGCE267 TIGLLMSSMD277 DLIRHCNGKL287 GSYKINGRTK 297 AMVACYPGNG307 TGYVRHVDNP317 NGDGRCVTCI327 YYLNKDWDAK337 VSGGILRIFP 347 EGKAQFADIE357 PKFDRLLFFW367 SDRRNPHEVQ377 PAYATRYAIT387 VWYFDADERA 397 RAKVKGVRV
|
|||||
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UN9 or .UN92 or .UN93 or :3UN9;style chemicals stick;color identity;select .A:254 or .A:256 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:327 or .A:329 or .A:343 or .A:374 or .A:376 or .A:383 or .A:385 or .A:389; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 3HQU PHD2:Fe:UN9:partial HIF1-alpha substrate complex | ||||||
Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [7] |
PDB Sequence |
LPALKLALEY
197 IVPCMNKHGI207 CVVDDFLGKE217 TGQQIGDEVR227 ALHDTGKFTD237 GQLVSQKSDS 247 SKDIRGDKIT257 WIEGKEPGCE267 TIGLLMSSMD277 DLIRHCNGKL287 GSYKINGRTK 297 AMVACYPGNG307 TGYVRHVDNP317 NGDGRCVTCI327 YYLNKDWDAK337 VSGGILRIFP 347 EGKAQFADIE357 PKFDRLLFFW367 SDRRNPHEVQ377 PAYATRYAIT387 VWYFDADERA 397 RAKVK
|
|||||
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UN9 or .UN92 or .UN93 or :3UN9;style chemicals stick;color identity;select .A:254 or .A:256 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:327 or .A:329 or .A:343 or .A:374 or .A:376 or .A:383 or .A:385 or .A:389; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 6YW2 HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic FG2216 and RaPID-derived cyclic peptide 3C (14-mer) | ||||||
Method | X-ray diffraction | Resolution | 2.14 Å | Mutation | No | [8] |
PDB Sequence |
TKPLPALKLA
194 LEYIVPCMNK204 HGICVVDDFL214 GKETGQQIGD224 EVRALHDTGK234 FTDGIRGDKI 256 TWIEGKEPGC266 ETIGLLMSSM276 DDLIRHCNGK286 LGSYKINGRT296 KAMVACYPGN 306 GTGYVRHVDN316 PNGDGRCVTC326 IYYLNKDWDA336 KVSGGILRIF346 PEGKAQFADI 356 EPKFDRLLFF366 WSDRRNPHEV376 QPAYATRYAI386 TVWYFDADER396 ARAKVKYLT |
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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 .UN9 or .UN92 or .UN93 or :3UN9;style chemicals stick;color identity;select .A:238 or .A:254 or .A:256 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:322 or .A:327 or .A:329 or .A:343 or .A:358 or .A:364 or .A:366 or .A:374 or .A:375 or .A:376 or .A:383 or .A:385 or .A:387 or .A:389; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY238
3.391
ASP254
2.268
ILE256
2.377
MET299
2.821
ALA301
3.402
TYR303
1.759
TYR310
3.178
HIS313
2.823
ASP315
3.244
ARG322
4.432
ILE327
2.625
TYR329
1.790
|
References | Top | ||||
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REF 1 | Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases. Nat Commun. 2016 Aug 26;7:12673. | ||||
REF 2 | Investigating the contribution of the active site environment to the slow reaction of hypoxia-inducible factor prolyl hydroxylase domain 2 with oxygen. Biochem J. 2014 Nov 1;463(3):363-72. | ||||
REF 3 | Selective small molecule probes for the hypoxia inducible factor (HIF) prolyl hydroxylases. ACS Chem Biol. 2013 Jul 19;8(7):1488-96. | ||||
REF 4 | Studies on the reaction of nitric oxide with the hypoxia-inducible factor prolyl hydroxylase domain 2 (EGLN1). J Mol Biol. 2011 Jul 8;410(2):268-79. | ||||
REF 5 | Crystal structure of HIF prolyl hydroxylase in complex with a biologically active inhibitor | ||||
REF 6 | Crystal structure of HIF prolyl hydroxylase in complex with a biologically active inhibitor | ||||
REF 7 | Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases. Structure. 2009 Jul 15;17(7):981-9. | ||||
REF 8 | Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2. Sci Rep. 2020 Dec 15;10(1):21964. |
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