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 | 6-Hydroxyuridine-5'-Phosphate | Ligand Info | |||
| Canonical SMILES | C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)O | ||||
| InChI | 1S/C9H13N2O10P/c12-4-1-5(13)11(9(16)10-4)8-7(15)6(14)3(21-8)2-20-22(17,18)19/h1,3,6-8,13-15H,2H2,(H,10,12,16)(H2,17,18,19)/t3-,6-,7-,8-/m1/s1 | ||||
| InChIKey | UDOBICLZEKUKCV-YXZULKJRSA-N | ||||
| PubChem Compound ID | 161647 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 3BGG Crystal structure of Human Orotidine 5'-monophosphate Decarboxylase complexed with BMP | ||||||
| Method | X-ray diffraction | Resolution | 1.93 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 |
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|
|
SER68
3.076
ASP70
2.697
LYS92
2.868
HIS94
3.056
ASP123
3.298
LYS125
2.656
ASN152
4.791
GLU181
4.173
MET182
3.078
SER183
2.742
SER184
4.702
|
|||||
| PDB ID: 7OTU Human OMPD-domain of UMPS in complex with 6-hydroxy-UMP at 0.95 Angstroms resolution, crystal 2 | ||||||
| Method | X-ray diffraction | Resolution | 0.95 Å | Mutation | No | [2] |
| 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 |
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|
|
SER257
2.514
ASP259
2.062
LYS281
2.040
HIS283
2.368
ASP312
2.843
LYS314
1.839
ASN341
4.392
ILE368
4.966
GLU370
4.172
MET371
2.379
SER372
1.798
SER373
4.183
|
|||||
| PDB ID: 6YWT Human OMPD-domain of UMPS (K314AcK) in complex with 6-hydroxy-UMP at 1.05 Angstroms resolution | ||||||
| Method | X-ray diffraction | Resolution | 1.05 Å | Mutation | No | [2] |
| 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 |
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|
|
SER257
3.162
ASP259
2.695
LYS281
2.829
HIS283
2.953
ASP312
2.567
ASN341
4.719
GLU370
4.252
MET371
3.280
SER372
2.788
SER373
4.930
ILE401
3.961
|
|||||
| PDB ID: 3EX4 human orotidyl-5'-monophosphate decarboxylase in complex with BMP | ||||||
| Method | X-ray diffraction | Resolution | 1.24 Å | Mutation | No | [3] |
| 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 |
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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 .BMP or .BMP2 or .BMP3 or :3BMP;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:341 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
3.155
ASP259
2.707
LYS281
2.897
HIS283
3.001
ASP312
3.288
LYS314
2.681
ASN341
4.885
GLU370
4.142
MET371
3.080
SER372
2.818
SER373
4.802
|
|||||
| PDB ID: 3EWX K314A mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-azido-UMP, degraded to BMP | ||||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | Yes | [3] |
| 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 .BMP or .BMP2 or .BMP3 or :3BMP;style chemicals stick;color identity;select .A:257 or .A:259 or .A:281 or .A:283 or .A:312 or .A:341 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
3.179
ASP259
2.755
LYS281
2.916
HIS283
2.989
ASP312
2.883
ASN341
4.759
GLU370
4.220
MET371
3.185
SER372
2.732
SER373
4.873
ILE401
4.198
|
|||||
| PDB ID: 7OUZ Human OMPD-domain of UMPS in complex with 6-hydroxy-UMP at 0.9 Angstroms resolution, crystal 1 | ||||||
| Method | X-ray diffraction | Resolution | 0.90 Å | Mutation | No | [2] |
| 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 |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BMP or .BMP2 or .BMP3 or :3BMP;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:341 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
2.505
ASP259
2.431
LYS281
2.037
HIS283
2.417
ASP312
2.833
LYS314
1.820
ASN341
4.389
ILE368
4.975
GLU370
4.171
MET371
2.372
SER372
1.820
SER373
4.202
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Crystal structure of Human Orotidine 5'-monophosphate Decarboxylase complexed with BMP | ||||
| REF 2 | 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 3 | Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase. Chemistry. 2009 Jul 6;15(27):6619-25. | ||||
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