Structure of PDB 6yvo Chain A Binding Site BS01

Receptor Information
>6yvo Chain A (length=256) 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
YLSRLG
Ligand information
Ligand IDOMP
InChIInChI=1S/C10H13N2O11P/c13-5-1-3(9(16)17)12(10(18)11-5)8-7(15)6(14)4(23-8)2-22-24(19,20)21/h1,4,6-8,14-15H,2H2,(H,16,17)(H,11,13,18)(H2,19,20,21)/t4-,6-,7-,8-/m1/s1
InChIKeyKYOBSHFOBAOFBF-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)C(=O)O
CACTVS 3.385O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2C(O)=O
OpenEye OEToolkits 1.7.5C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C(=O)O
CACTVS 3.385O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2C(O)=O
ACDLabs 10.04O=C(O)C=1N(C(=O)NC(=O)C=1)C2OC(C(O)C2O)COP(=O)(O)O
FormulaC10 H13 N2 O11 P
NameOROTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL1207358
DrugBankDB02957
ZINCZINC000004095542
PDB chain6yvo Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6yvo Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5-monophosphate decarboxylase catalysis
Resolution1.25 Å
Binding residue
(original residue number in PDB)		S257 D259 K281 H283 D312 K314 M371 S372 P417 Q430 Y432 G450 R451
Binding residue
(residue number reindexed from 1)		S34 D36 K58 H60 D89 K91 M148 S149 P194 Q207 Y209 G227 R228
Annotation score4
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:6yvo, PDBe:6yvo, PDBj:6yvo
PDBsum6yvo
PubMed
UniProtP11172|UMPS_HUMAN Uridine 5'-monophosphate synthase (Gene Name=UMPS)

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