Structure of PDB 3thq Chain A Binding Site BS01

Receptor Information
>3thq Chain A (length=216) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIA
EFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVR
ACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGP
STRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYL
ADNPAAAAAGIIESIK
Ligand information
Ligand IDNUP
InChIInChI=1S/C9H14N3O9P/c10-4-1-5(13)11-9(16)12(4)8-7(15)6(14)3(21-8)2-20-22(17,18)19/h1,3,6-8,14-15H,2,10H2,(H,11,13,16)(H2,17,18,19)/t3-,6-,7-,8-/m1/s1
InChIKeyDUFXRFNPGXQQOI-YXZULKJRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)N
CACTVS 3.341NC1=CC(=O)NC(=O)N1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04O=C1NC(=O)N(C(N)=C1)C2OC(C(O)C2O)COP(=O)(O)O
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)N
CACTVS 3.341NC1=CC(=O)NC(=O)N1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
FormulaC9 H14 N3 O9 P
Name6-AMINOURIDINE 5'-MONOPHOSPHATE
ChEMBLCHEMBL514137
DrugBank
ZINCZINC000014975890
PDB chain3thq Chain A Residue 1000 [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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PDB3thq Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase complexed with 6-amino-UMP
Resolution1.5 Å
Binding residue
(original residue number in PDB)		D20 K42 D70 K72 M126 S127 P180 Q185 G202 R203
Binding residue
(residue number reindexed from 1)		D13 K35 D63 K65 M119 S120 P173 Q178 G195 R196
Annotation score2
Binding affinityBindingDB: Ki=840nM
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 K72 D75
Catalytic site (residue number reindexed from 1) K35 D63 K65 D68
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:0044205 'de novo' UMP 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:3thq, PDBe:3thq, PDBj:3thq
PDBsum3thq
PubMed
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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