Structure of PDB 3g3d Chain B Binding Site BS02

Receptor Information
>3g3d Chain B (length=259) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APKELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLA
DALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGN
TVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAE
MSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQ
LEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAA
WEAYLSRLG
Ligand information
Ligand ID5FU
InChIInChI=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
InChIKeyRNBMPPYRHNWTMA-UAKXSSHOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)F
OpenEye OEToolkits 1.5.0C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)F
ACDLabs 10.04FC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2O)COP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(F)C(=O)NC2=O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(F)C(=O)NC2=O
FormulaC9 H12 F N2 O9 P
Name5-FLUORO-URIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL474163
DrugBank
ZINC
PDB chain3g3d Chain B Residue 3000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3g3d Structure-activity relationships of orotidine-5'-monophosphate decarboxylase inhibitors as anticancer agents.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		S68 D70 H94 K125 M182 S183 P228 Q241 Y243 G261 R262
Binding residue
(residue number reindexed from 1)		S37 D39 H63 K94 M151 S152 P197 Q210 Y212 G230 R231
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=4.74,Ki=18.2uM
BindingDB: Ki=98000nM
Enzymatic activity
Enzyme Commision number 2.4.2.10: orotate phosphoribosyltransferase.
4.1.1.23: orotidine-5'-phosphate decarboxylase.
Gene Ontology
Molecular Function
GO:0004590 orotidine-5'-phosphate decarboxylase activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0044205 'de novo' UMP biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3g3d, PDBe:3g3d, PDBj:3g3d
PDBsum3g3d
PubMed19260677
UniProtP11172|UMPS_HUMAN Uridine 5'-monophosphate synthase (Gene Name=UMPS)

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