Structure of PDB 3l0n Chain A Binding Site BS01

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 A Residue 257 [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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PDB3l0n Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase
Resolution1.74 Å
Binding residue
(original residue number in PDB)		S33 D35 K57 H59 D88 K90 M147 S148 P193 Q206 Y208 G226 R227
Binding residue
(residue number reindexed from 1)		S34 D36 K58 H60 D89 K91 M148 S149 P194 Q207 Y209 G227 R228
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

View graph for
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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