Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
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
UMPS_HUMAN
Ligand General Information  Top
Ligand Name 5-Fluorouridine monophosphate Ligand Info
Canonical SMILES C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)F
InChI 1S/C9H12FN2O9P/c10-3-1-12(9(16)11-7(3)15)8-6(14)5(13)4(21-8)2-20-22(17,18)19/h1,4-6,8,13-14H,2H2,(H,11,15,16)(H2,17,18,19)/t4-,5-,6-,8-/m1/s1
InChIKey RNBMPPYRHNWTMA-UAKXSSHOSA-N
PubChem Compound ID 150856
Drug Binding Sites of Target  Top
PDB ID: 3G3D      Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 5-fluoro-6-azido-UMP
Method X-ray diffraction Resolution 1.70 Å Mutation No [1]
PDB Sequence
ELSFGARAEL
44
PRIHPVASKL
54
LRLMQKKETN
64
LCLSADVSLA
74
RELLQLADAL
84

GPSICMLKTH
94
VDILNDFTLD
104
VMKELITLAK
114
CHEFLIFEDR
124
KFADIGNTVK
134

KQYEGGIFKI
144
ASWADLVNAH
154
VVPGSGVVKG
164
LQEVGLPLHR
174
GCLLIAEMSS
184

TGSLATGDYT
194
RAAVRMAEEH
204
SEFVVGFISG
214
SRVSMKPEFL
224
HLTPGVQLEA
234

GGDNLGQQYN
244
SPQEVIGKRG
254
SDIIIVGRGI
264
ISAADRLEAA
274
EMYRKAAWEA
284

YLSRLG
Residue
Distance (Å)
SER68
3.167
ASP70
2.842
LYS92
2.954
HIS94
2.967
ASP123
3.629
LYS125
1.381
ILE179
4.175
GLU181
4.126
MET182
3.057
SER183
2.720
SER184
4.932
Residue
Distance (Å)
ILE212
4.044
PRO228
3.405
GLY229
4.329
VAL230
4.408
GLN241
2.941
TYR243
2.695
ILE259
4.551
VAL260
3.912
GLY261
2.813
ARG262
2.832
GLY263
4.775
PDB ID: 3MW7      Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-UMP(produced from 5-fluoro-6-amino-UMP)
Method X-ray diffraction Resolution 2.32 Å Mutation No [2]
PDB Sequence
APKELSFGAR
41
AELPRIHPVA
51
SKLLRLMQKK
61
ETNLCLSADV
71
SLARELLQLA
81

DALGPSICML
91
KTHVDILNDF
101
TLDVMKELIT
111
LAKCHEFLIF
121
EDRKFADIGN
131

TVKKQYEGGI
141
FKIASWADLV
151
NAHVVPGSGV
161
VKGLQEVGLP
171
LHRGCLLIAE
181

MSSTGSLATG
191
DYTRAAVRMA
201
EEHSEFVVGF
211
ISGSRVSMKP
221
EFLHLTPGVQ
231

LEAGGDNLGQ
241
QYNSPQEVIG
251
KRGSDIIIVG
261
RGIISAADRL
271
EAAEMYRKAA
281

WEAYLSRLG
Residue
Distance (Å)
SER68
3.082
ASP70
2.793
LYS92
3.210
HIS94
2.917
ASP123
3.615
LYS125
2.907
ILE179
4.473
GLU181
4.509
MET182
3.394
SER183
3.079
ILE212
3.523
Residue
Distance (Å)
PRO228
3.384
GLY229
4.638
VAL230
4.543
GLN241
2.847
TYR243
2.719
ILE259
4.073
VAL260
3.716
GLY261
2.734
ARG262
2.828
GLY263
4.859
PDB ID: 3G3M      Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 5-fluoro-6-iodo-UMP
Method X-ray diffraction Resolution 1.40 Å Mutation No [1]
PDB Sequence
KELSFGARAE
43
LPRIHPVASK
53
LLRLMQKKET
63
NLCLSADVSL
73
ARELLQLADA
83

LGPSICMLKT
93
HVDILNDFTL
103
DVMKELITLA
113
KHEFLIFEDR
124
KFADIGNTVK
134

KQYEGGIFKI
144
ASWADLVNAH
154
VVPGSGVVKG
164
LQEVGLPLHR
174
GCLLIAEMSS
184

TGSLATGDYT
194
RAAVRMAEEH
204
SEFVVGFISG
214
SRVSMKPEFL
224
HLTPGVQLEA
234

GGDNLGQQYN
244
SPQEVIGKRG
254
SDIIIVGRGI
264
ISAADRLEAA
274
EMYRKAAWEA
284

YLSRLG
Residue
Distance (Å)
SER68
3.167
ASP70
2.708
LYS92
2.909
HIS94
2.960
ASP123
3.464
LYS125
1.290
ILE179
4.227
GLU181
4.110
MET182
3.155
SER183
2.755
SER184
4.980
Residue
Distance (Å)
ILE212
4.064
PRO228
3.341
GLY229
4.464
VAL230
4.406
GLN241
2.842
TYR243
2.704
ILE259
4.436
VAL260
4.009
GLY261
2.913
ARG262
2.769
GLY263
4.806
PDB ID: 2QCF      Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to 5-fluoro-UMP
Method X-ray diffraction Resolution 1.22 Å Mutation Yes [3]
PDB Sequence
MELSFGARAE
232
LPRIHPVASK
242
LLRLMQKKET
252
NLCLSADVSL
262
ARELLQLADA
272

LGPSICMLKT
282
HVDILNDFTL
292
DVMKELITLA
302
KHEFLIFENR
313
KFADIGNTVK
323

KQYEGGIFKI
333
ASWADLVNAH
343
VVPGSGVVKG
353
LQEVGLPLHR
363
GCLLIAEMSS
373

TGSLATGDYT
383
RAAVRMAEEH
393
SEFVVGFISG
403
SRVSMKPEFL
413
HLTPGVQLEA
423

GGDNLGQQYN
433
SPQEVIGKRG
443
SDIIIVGRGI
453
ISAADRLEAA
463
EMYRKAAWEA
473

YLSRLG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5FU or .5FU2 or .5FU3 or :35FU;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: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
Residue
Distance (Å)
SER257
3.146
ASP259
2.732
LYS281
2.857
HIS283
3.032
ASN312
3.505
LYS314
3.102
ASN341
4.838
ILE368
4.371
GLU370
4.206
MET371
3.138
SER372
2.726
SER373
4.998
Residue
Distance (Å)
ILE401
3.615
PRO417
3.304
GLY418
4.319
VAL419
4.377
GLN430
2.875
TYR432
2.659
ILE448
3.969
VAL449
3.937
GLY450
2.854
ARG451
2.720
GLY452
4.704
References  Top
REF 1 Structure-activity relationships of orotidine-5'-monophosphate decarboxylase inhibitors as anticancer agents. J Med Chem. 2009 Mar 26;52(6):1648-58.
REF 2 Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-UMP(produced from 5-fluoro-6-amino-UMP)
REF 3 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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