Structure of PDB 1dqx Chain D Binding Site BS02

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 D Residue 604 [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)		S35 D37 K59 H61 D91 K93 L153 S154 P202 Q215 Y217 G234 R235
Binding residue
(residue number reindexed from 1)		S35 D37 K59 H61 D91 K93 L153 S154 P202 Q215 Y217 G234 R235
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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