Structure of PDB 3l0n Chain A Binding Site BS02

Receptor Information
>3l0n Chain A (length=255) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADAL
GPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVK
KQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSS
TGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEA
GGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEA
YLSRL
Ligand information
Ligand IDS5P
InChIInChI=1S/C9H13N2O9PS/c12-4-1-5(22)11(9(15)10-4)8-7(14)6(13)3(20-8)2-19-21(16,17)18/h1,3,6-8,13-14,22H,2H2,(H,10,12,15)(H2,16,17,18)/t3-,6-,7-,8-/m1/s1
InChIKeyVNOFOHWXLQGLEX-YXZULKJRSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=CC(=O)NC2=O)S
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=CC(=O)NC2=O)S
ACDLabs 10.04O=C1NC(=O)N(C(S)=C1)C2OC(C(O)C2O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)S
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)S
FormulaC9 H13 N2 O9 P S
Name6-sulfanyluridine-5'-phosphate;
6-mercaptouridine-5'-monophosphate
ChEMBL
DrugBank
ZINCZINC000103556152
PDB chain3l0n Chain B Residue 257 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3l0n Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase
Resolution1.74 Å
Binding residue
(original residue number in PDB)		D93 I94 T97
Binding residue
(residue number reindexed from 1)		D94 I95 T98
Annotation score2
Binding affinityMOAD: ic50=1680uM
PDBbind-CN: -logKd/Ki=2.77,IC50=1680uM
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3l0n, PDBe:3l0n, PDBj:3l0n
PDBsum3l0n
PubMed19472232
UniProtP11172|UMPS_HUMAN Uridine 5'-monophosphate synthase (Gene Name=UMPS)

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