Structure of PDB 1dqx Chain D Binding Site BS01

Receptor Information
>1dqx Chain D (length=267) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEA
LGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNT
VKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLML
AELSCKGSLSTGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIM
TPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGER
YRKAGWEAYLRRCGQQD
Ligand information
Ligand IDBMP
InChIInChI=1S/C9H13N2O10P/c12-4-1-5(13)11(9(16)10-4)8-7(15)6(14)3(21-8)2-20-22(17,18)19/h1,3,6-8,13-15H,2H2,(H,10,12,16)(H2,17,18,19)/t3-,6-,7-,8-/m1/s1
InChIKeyUDOBICLZEKUKCV-YXZULKJRSA-N
SMILES
SoftwareSMILES
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)O
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2O
ACDLabs 10.04O=C1NC(=O)N(C(O)=C1)C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H13 N2 O10 P
Name6-HYDROXYURIDINE-5'-PHOSPHATE
ChEMBLCHEMBL383923
DrugBankDB02890
ZINCZINC000024479522
PDB chain1dqx Chain C Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1dqx Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D96 I97 T100
Binding residue
(residue number reindexed from 1)		D96 I97 T100
Annotation score3
Binding affinityMOAD: Ki=9pM
BindingDB: Ki=0.0090nM
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:1dqx, PDBe:1dqx, PDBj:1dqx
PDBsum1dqx
PubMed10681417
UniProtP03962|PYRF_YEAST Orotidine 5'-phosphate decarboxylase (Gene Name=URA3)

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