Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T15851 | Target Info | |||
| Target Name | Orotidine 5'-monophosphate decarboxylase (UMPS) | ||||
| Synonyms | Uridine 5'-monophosphate synthase; UMP synthase | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | UMPS | ||||
| Biochemical Class | Pentosyltransferase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Uridine-5'-Monophosphate | Ligand Info | |||
| Canonical SMILES | C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O | ||||
| InChI | 1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 | ||||
| InChIKey | DJJCXFVJDGTHFX-XVFCMESISA-N | ||||
| PubChem Compound ID | 6030 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 3BGJ Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 6-iodo-UMP | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
KELSFGARAE
43 LPRIHPVASK53 LLRLMQKKET63 NLCLSADVSL73 ARELLQLADA83 LGPSICMLKT 93 HVDILNDFTL103 DVMKELITLA113 KCHEFLIFED123 RKFADIGNTV133 KKQYEGGIFK 143 IASWADLVNA153 HVVPGSGVVK163 GLQEVGLPLH173 RGCLLIAEMS183 STGSLATGDY 193 TRAAVRMAEE203 HSEFVVGFIS213 GSRVSMKPEF223 LHLTPGVQLE233 AGGDNLGQQY 243 NSPQEVIGKR253 GSDIIIVGRG263 IISAADRLEA273 AEMYRKAAWE283 AYLSRLG |
|||||
|
|
SER68
3.293
ASP70
2.829
LYS92
2.822
HIS94
2.921
ASP123
3.391
LYS125
1.298
GLU181
4.255
MET182
3.194
SER183
2.767
SER184
4.901
ILE212
4.444
|
|||||
| PDB ID: 2V30 Human orotidine 5'-phosphate decarboxylase domain of uridine monophospate synthetase (UMPS) in complex with its product UMP. | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [2] |
| PDB Sequence |
LYFQSMELSF
227 GARAELPRIH237 PVASKLLRLM247 QKKETNLCLS257 ADVSLARELL267 QLADALGPSI 277 CMLKTHVDIL287 NDFTLDVMKE297 LITLAKCHEF307 LIFEDRKFAD317 IGNTVKKQYE 327 GGIFKIASWA337 DLVNAHVVPG347 SGVVKGLQEV357 GLPLHRGCLL367 IAEMSSTGSL 377 ATGDYTRAAV387 RMAEEHSEFV397 VGFISGSRVS407 MKPEFLHLTP417 GVQLEAGGDN 427 LGQQYNSPQE437 VIGKRGSDII447 IVGRGIISAA457 DRLEAAEMYR467 KAAWEAYLSR 477 LG
|
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|
|
SER257
3.031
ASP259
2.700
LYS281
2.849
HIS283
3.214
ASP312
3.687
LYS314
3.088
GLU370
4.322
MET371
3.207
SER372
2.886
SER373
4.947
ILE401
4.206
|
|||||
| PDB ID: 6ZWY OMPD-domain of human UMPS in complex with UMP at 1.0 Angstroms resolution | ||||||
| Method | X-ray diffraction | Resolution | 1.00 Å | Mutation | No | [3] |
| PDB Sequence |
MELSFGARAE
232 LPRIHPVASK242 LLRLMQKKET252 NLCLSADVSL262 ARELLQLADA272 LGPSICMLKT 282 HVDILNDFTL292 DVMKELITLA302 KHEFLIFEDR313 KFADIGNTVK323 KQYEGGIFKI 333 ASWADLVNAH343 VVPGSGVVKG353 LQEVGLPLHR363 GCLLIAEMSS373 TGSLATGDYT 383 RAAVRMAEEH393 SEFVVGFISG403 SRVSMKPEFL413 HLTPGVQLEA423 GGDNLGQQYN 433 SPQEVIGKRG443 SDIIIVGRGI453 ISAADRLEAA463 EMYRKAAWEA473 YLSRLG |
|||||
|
|
SER257
3.145
ASP259
2.693
LYS281
2.867
HIS283
3.006
ASP312
3.710
LYS314
3.233
GLU370
4.275
MET371
3.123
SER372
2.838
SER373
4.834
ILE401
4.221
|
|||||
| PDB ID: 3EWY K314A mutant of human orotidyl-5'-monophosphate decarboxylase soaked with OMP, decarboxylated to UMP | ||||||
| Method | X-ray diffraction | Resolution | 1.10 Å | Mutation | Yes | [4] |
| PDB Sequence |
MELSFGARAE
232 LPRIHPVASK242 LLRLMQKKET252 NLCLSADVSL262 ARELLQLADA272 LGPSICMLKT 282 HVDILNDFTL292 DVMKELITLA302 KHEFLIFEDR313 AFADIGNTVK323 KQYEGGIFKI 333 ASWADLVNAH343 VVPGSGVVKG353 LQEVGLPLHR363 GCLLIAEMSS373 TGSLATGDYT 383 RAAVRMAEEH393 SEFVVGFISG403 SRVSMKPEFL413 HLTPGVQLEA423 GGDNLGQQYN 433 SPQEVIGKRG443 SDIIIVGRGI453 ISAADRLEAA463 EMYRKAAWEA473 YLSRLG |
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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 .U5P or .U5P2 or .U5P3 or :3U5P;style chemicals stick;color identity;select .A:257 or .A:259 or .A:281 or .A:283 or .A:312 or .A:370 or .A:371 or .A:372 or .A:373 or .A:401 or .A:417 or .A:418 or .A:419 or .A:430 or .A:432 or .A:448 or .A:449 or .A:450 or .A:451 or .A:452; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER257
3.194
ASP259
2.755
LYS281
2.893
HIS283
2.936
ASP312
3.537
GLU370
4.267
MET371
3.161
SER372
2.772
SER373
4.865
ILE401
4.323
|
|||||
| PDB ID: 6YWU Human OMPD-domain of UMPS (K314AcK) in complex with UMP at 1.1 Angstroms resolution | ||||||
| Method | X-ray diffraction | Resolution | 1.10 Å | Mutation | No | [3] |
| PDB Sequence |
ELSFGARAEL
233 PRIHPVASKL243 LRLMQKKETN253 LCLSADVSLA263 RELLQLADAL273 GPSICMLKTH 283 VDILNDFTLD293 VMKELITLAK303 HEFLIFEDRF315 ADIGNTVKKQ325 YEGGIFKIAS 335 WADLVNAHVV345 PGSGVVKGLQ355 EVGLPLHRGC365 LLIAEMSSTG375 SLATGDYTRA 385 AVRMAEEHSE395 FVVGFISGSR405 VSMKPEFLHL415 TPGVQLEAGG425 DNLGQQYNSP 435 QEVIGKRGSD445 IIIVGRGIIS455 AADRLEAAEM465 YRKAAWEAYL475 SRLG |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .U5P or .U5P2 or .U5P3 or :3U5P;style chemicals stick;color identity;select .A:257 or .A:259 or .A:281 or .A:283 or .A:312 or .A:370 or .A:371 or .A:372 or .A:401 or .A:417 or .A:418 or .A:419 or .A:430 or .A:432 or .A:448 or .A:449 or .A:450 or .A:451 or .A:452; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 3EX1 human orotidyl-5'-monophosphate decarboxylase soaked with 6-cyano-UMP, converted to UMP | ||||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | No | [4] |
| PDB Sequence |
MELSFGARAE
232 LPRIHPVASK242 LLRLMQKKET252 NLCLSADVSL262 ARELLQLADA272 LGPSICMLKT 282 HVDILNDFTL292 DVMKELITLA302 KCHEFLIFED312 RKFADIGNTV322 KKQYEGGIFK 332 IASWADLVNA342 HVVPGSGVVK352 GLQEVGLPLH362 RGCLLIAEMS372 STGSLATGDY 382 TRAAVRMAEE392 HSEFVVGFIS402 GSRVSMKPEF412 LHLTPGVQLE422 AGGDNLGQQY 432 NSPQEVIGKR442 GSDIIIVGRG452 IISAADRLEA462 AEMYRKAAWE472 AYLSRLG |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .U5P or .U5P2 or .U5P3 or :3U5P;style chemicals stick;color identity;select .A:257 or .A:259 or .A:281 or .A:283 or .A:312 or .A:314 or .A:370 or .A:371 or .A:372 or .A:373 or .A:401 or .A:417 or .A:418 or .A:419 or .A:430 or .A:432 or .A:448 or .A:449 or .A:450 or .A:451 or .A:452; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER257
3.103
ASP259
2.696
LYS281
2.845
HIS283
2.984
ASP312
3.547
LYS314
2.958
GLU370
4.337
MET371
3.303
SER372
2.733
SER373
4.919
ILE401
4.389
|
|||||
| PDB ID: 3EX3 human orotidyl-5'-monophosphate decarboxylase in complex with 6-azido-UMP, covalent adduct | ||||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [4] |
| PDB Sequence |
MELSFGARAE
232 LPRIHPVASK242 LLRLMQKKET252 NLCLSADVSL262 ARELLQLADA272 LGPSICMLKT 282 HVDILNDFTL292 DVMKELITLA302 KCHEFLIFED312 RKFADIGNTV322 KKQYEGGIFK 332 IASWADLVNA342 HVVPGSGVVK352 GLQEVGLPLH362 RGCLLIAEMS372 STGSLATGDY 382 TRAAVRMAEE392 HSEFVVGFIS402 GSRVSMKPEF412 LHLTPGVQLE422 AGGDNLGQQY 432 NSPQEVIGKR442 GSDIIIVGRG452 IISAADRLEA462 AEMYRKAAWE472 AYLSRLG |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .U5P or .U5P2 or .U5P3 or :3U5P;style chemicals stick;color identity;select .A:257 or .A:259 or .A:281 or .A:283 or .A:312 or .A:314 or .A:370 or .A:371 or .A:372 or .A:373 or .A:401 or .A:417 or .A:418 or .A:419 or .A:430 or .A:432 or .A:448 or .A:449 or .A:450 or .A:451 or .A:452; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER257
3.180
ASP259
2.608
LYS281
2.901
HIS283
3.057
ASP312
3.368
LYS314
1.429
GLU370
4.215
MET371
3.238
SER372
2.837
SER373
4.978
ILE401
4.391
|
|||||
| PDB ID: 2QCN Covalent complex of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase with 6-iodo-UMP | ||||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [5] |
| PDB Sequence |
MELSFGARAE
232 LPRIHPVASK242 LLRLMQKKET252 NLCLSADVSL262 ARELLQLADA272 LGPSICMLKT 282 HVDILNDFTL292 DVMKELITLA302 KCHEFLIFED312 RKFADIGNTV322 KKQYEGGIFK 332 IASWADLVNA342 HVVPGSGVVK352 GLQEVGLPLH362 RGCLLIAEMS372 STGSLATGDY 382 TRAAVRMAEE392 HSEFVVGFIS402 GSRVSMKPEF412 LHLTPGVQLE422 AGGDNLGQQY 432 NSPQEVIGKR442 GSDIIIVGRG452 IISAADRLEA462 AEMYRKAAWE472 AYLSRLG |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .U5P or .U5P2 or .U5P3 or :3U5P;style chemicals stick;color identity;select .A:257 or .A:259 or .A:281 or .A:283 or .A:312 or .A:314 or .A:370 or .A:371 or .A:372 or .A:373 or .A:401 or .A:417 or .A:418 or .A:419 or .A:430 or .A:432 or .A:448 or .A:449 or .A:450 or .A:451 or .A:452; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER257
3.280
ASP259
2.779
LYS281
2.857
HIS283
3.037
ASP312
3.312
LYS314
1.452
GLU370
4.234
MET371
3.220
SER372
2.743
SER373
4.927
ILE401
4.351
|
|||||
| PDB ID: 2QCD Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to UMP | ||||||
| Method | X-ray diffraction | Resolution | 2.03 Å | Mutation | No | [5] |
| PDB Sequence |
> Chain A
AMELSFGARA 231 ELPRIHPVAS241 KLLRLMQKKE251 TNLCLSADVS261 LARELLQLAD271 ALGPSICMLK 281 THVDILNDFT291 LDVMKELITL301 AKHEFLIFED312 RKFADIGNTV322 KKQYEGGIFK 332 IASWADLVNA342 HVVPGSGVVK352 GLQEVGLPLH362 RGCLLIAEMS372 STGSLATGDY 382 TRAAVRMAEE392 HSEFVVGFIS402 GSRVSMKPEF412 LHLTPGVQLE422 AGGDNLGQQY 432 NSPQEVIGKR442 GSDIIIVGRG452 IISAADRLEA462 AEMYRKAAWE472 AYLSRLG > Chain B AMELSFGARA 231 ELPRIHPVAS241 KLLRLMQKKE251 TNLCLSADVS261 LARELLQLAD271 ALGPSICMLK 281 THVDILNDFT291 LDVMKELITL301 AKCHEFLIFE311 DRKFADIGNT321 VKKQYEGGIF 331 KIASWADLVN341 AHVVPGSGVV351 KGLQEVGLPL361 HRGCLLIAEM371 SSTGSLATGD 381 YTRAAVRMAE391 EHSEFVVGFI401 SGSRVSMKPE411 FLHLTPGVQL421 EAGGDNLGQQ 431 YNSPQEVIGK441 RGSDIIIVGR451 GIISAADRLE461 AAEMYRKAAW471 EAYLSRLG |
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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 .U5P or .U5P2 or .U5P3 or :3U5P;style chemicals stick;color identity;select .A:257 or .A:259 or .A:281 or .A:283 or .A:312 or .A:314 or .A:370 or .A:371 or .A:372 or .A:373 or .A:401 or .A:417 or .A:418 or .A:419 or .A:430 or .A:432 or .A:448 or .A:449 or .A:450 or .A:451 or .A:452 or .A:317 or .A:318 or .A:321 or .B:317 or .B:318 or .B:321 or .B:257 or .B:259 or .B:281 or .B:283 or .B:312 or .B:314 or .B:370 or .B:371 or .B:372 or .B:401 or .B:417 or .B:418 or .B:419 or .B:430 or .B:432 or .B:448 or .B:449 or .B:450 or .B:451 or .B:452; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER257[A]
3.083
ASP259[A]
2.659
LYS281[A]
2.725
HIS283[A]
3.072
ASP312[A]
3.646
LYS314[A]
3.063
GLU370[A]
4.360
MET371[A]
3.277
SER372[A]
2.719
SER373[A]
4.924
ILE401[A]
4.294
PRO417[A]
3.428
GLY418[A]
4.299
VAL419[A]
4.490
GLN430[A]
2.762
TYR432[A]
2.738
ILE448[A]
4.071
VAL449[A]
3.982
GLY450[A]
2.950
ARG451[A]
2.785
GLY452[A]
4.756
ASP317[A]
2.663
ILE318[A]
3.565
THR321[A]
2.846
ASP317[B]
2.665
ILE318[B]
3.476
THR321[B]
2.781
SER257[B]
3.132
ASP259[B]
2.678
LYS281[B]
2.904
HIS283[B]
3.060
ASP312[B]
3.658
LYS314[B]
3.136
GLU370[B]
4.241
MET371[B]
3.223
SER372[B]
2.718
ILE401[B]
4.264
PRO417[B]
3.389
GLY418[B]
4.374
VAL419[B]
4.451
GLN430[B]
2.787
TYR432[B]
2.852
ILE448[B]
4.025
VAL449[B]
4.137
GLY450[B]
3.082
ARG451[B]
2.706
GLY452[B]
4.869
|
|||||
| PDB ID: 7ASQ Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the reaction product UMP at 0.95 Angstrom resolution | ||||||
| Method | X-ray diffraction | Resolution | 0.95 Å | Mutation | No | [3] |
| PDB Sequence |
MELSFGARAE
232 LPRIHPVASK242 LLRLMQKKET252 NLCLSADVSL262 ARELLQLADA272 LGPSICMLKT 282 HVDILNDFTL292 DVMKELITLA302 KHEFLIFEDR313 KFADIGNTVK323 KQYEGGIFKI 333 ASWADLVNAH343 VVPGSGVVKG353 LQEVGLPLHR363 GCLLIAEMSS373 TGSLATGDYT 383 RAAVRMAEEH393 SEFVVGFISG403 SRVSMKPEFL413 HLTPGVQLEA423 GGDNLGQQYN 433 SPQEVIGKRG443 SDIIIVGRGI453 ISAADRLEAA463 EMYRKAAWEA473 YLSRL |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .U5P or .U5P2 or .U5P3 or :3U5P;style chemicals stick;color identity;select .A:257 or .A:259 or .A:281 or .A:283 or .A:312 or .A:314 or .A:368 or .A:370 or .A:371 or .A:372 or .A:373 or .A:401 or .A:417 or .A:418 or .A:419 or .A:420 or .A:430 or .A:432 or .A:448 or .A:449 or .A:450 or .A:451 or .A:452; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER257
2.607
ASP259
2.718
LYS281
2.014
HIS283
3.005
ASP312
3.650
LYS314
2.493
ILE368
4.937
GLU370
4.231
MET371
2.425
SER372
2.174
SER373
4.348
ILE401
3.338
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 6-iodo-UMP | ||||
| REF 2 | The Crystal Structure of Human Orotidine 5'-Decarboxylase Domain of Human Uridine Monophosphate Synthetase (Umps) | ||||
| REF 3 | Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5-monophosphate decarboxylase catalysis. doi:10.1038/s41929-022-00771-w. | ||||
| REF 4 | Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase. Chemistry. 2009 Jul 6;15(27):6619-25. | ||||
| REF 5 | Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design. Structure. 2008 Jan;16(1):82-92. | ||||
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