Structure of PDB 3gdl Chain B Binding Site BS02

Receptor Information
>3gdl Chain B (length=257) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPK
ICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQ
YSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELS
CKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGV
GLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKA
GWEAYLR
Ligand information
Ligand IDUP6
InChIInChI=1S/C8H12N3O9P/c12-4-1-9-11(8(15)10-4)7-6(14)5(13)3(20-7)2-19-21(16,17)18/h1,3,5-7,13-14H,2H2,(H,10,12,15)(H2,16,17,18)/t3-,5-,6-,7-/m1/s1
InChIKeyLRVZOSYMNMNQFR-SHUUEZRQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=NN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2N=CC(=O)NC2=O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2N=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=NN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N(N=CC(=O)N1)C2OC(C(O)C2O)COP(=O)(O)O
FormulaC8 H12 N3 O9 P
Name6-AZA URIDINE 5'-MONOPHOSPHATE;
6-AZA-UMP
ChEMBLCHEMBL463480
DrugBankDB03718
ZINCZINC000012503861
PDB chain3gdl Chain B Residue 301 [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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PDB3gdl Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		S35 D37 K59 H61 K93 L153 S154 P202 Q215 Y217 G234 R235
Binding residue
(residue number reindexed from 1)		S31 D33 K55 H57 K89 L149 S150 P198 Q211 Y213 G230 R231
Annotation score2
Binding affinityBindingDB: Ki=64nM
Enzymatic activity
Enzyme Commision number 4.1.1.23: orotidine-5'-phosphate decarboxylase.
Gene Ontology
Molecular Function
GO:0004590 orotidine-5'-phosphate decarboxylase activity
GO:0016831 carboxy-lyase activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006222 UMP biosynthetic process
GO:0044205 'de novo' UMP biosynthetic process
GO:0055086 nucleobase-containing small molecule metabolic process
GO:0072528 pyrimidine-containing compound biosynthetic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3gdl, PDBe:3gdl, PDBj:3gdl
PDBsum3gdl
PubMed19435314
UniProtP03962|PYRF_YEAST Orotidine 5'-phosphate decarboxylase (Gene Name=URA3)

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