Structure of PDB 3li0 Chain B Binding Site BS01

Receptor Information
>3li0 Chain B (length=224) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRRVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEG
MDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPG
ADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVK
NYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVG
ASIYLADNPAAAAAGIIESIKDLL
Ligand information
Ligand IDBMQ
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/h3,6-8,14-15H,1-2H2,(H,10,12,16)(H2,17,18,19)/t3-,6-,7-,8-/m1/s1
InChIKeyAODYJUNLDJOADV-YXZULKJRSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)CC(=O)NC2=O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)CC(=O)NC2=O
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)CC1=O)C(O)C2O
OpenEye OEToolkits 1.7.2C1C(=O)NC(=O)N(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.7.2C1C(=O)NC(=O)N(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
FormulaC9 H13 N2 O10 P
Name1-(5'-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC ACID
ChEMBLCHEMBL1231399
DrugBankDB03668
ZINCZINC000001559604
PDB chain3li0 Chain A Residue 229 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3li0 Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.
Resolution1.5 Å
Binding residue
(original residue number in PDB)
D75 I76 T79
Binding residue
(residue number reindexed from 1)
D73 I74 T77
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 K72 D75
Catalytic site (residue number reindexed from 1) K40 D68 K70 D73
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:3li0, PDBe:3li0, PDBj:3li0
PDBsum3li0
PubMed23030629
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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