Structure of PDB 3gdt Chain D Binding Site BS01

Receptor Information
>3gdt Chain D (length=252) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALG
PKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFENRKFADIGNTVK
LQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAE
LSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTP
GVGRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCG
QQ
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 chain3gdt Chain D 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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PDB3gdt Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		K59 K93 S154 G203 G234 R235
Binding residue
(residue number reindexed from 1)		K57 K91 S152 G201 G220 R221
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=7.19,Ki=64nM
BindingDB: 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3gdt, PDBe:3gdt, PDBj:3gdt
PDBsum3gdt
PubMed19435314
UniProtP03962|PYRF_YEAST Orotidine 5'-phosphate decarboxylase (Gene Name=URA3)

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