Structure of PDB 7bix Chain C Binding Site BS03

Receptor Information
>7bix Chain C (length=229) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGYSRVLLKLGGEMFGGGQVGLDPDVVAQVARQIADVVRGGVQIAVVIGG
GNFFRGAQLQQLGMERTRSDYMGMLGTVMNSLALQDFLEKEGIVTRVQTA
ITMGQVAEPYLPLRAVRHLEKGRVVIFGAGMGLPYFSTDTTAAQRALEIG
ADVVLMAKAVDGVFAEDPAELLTAVSHREVLDRGLRVADATAFSLCMDNG
MPILVFNLLTDGNIARAVRGEKIGTLVTT
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain7bix Chain C Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7bix Structural basis for the allosteric inhibition of UMP kinase from Gram-positive bacteria, a promising antibacterial target.
Resolution3.12 Å
Binding residue
(original residue number in PDB)		K36 G39 G77 G78 R82 G83 D97 G100 M101 M158 L160 F163 T165
Binding residue
(residue number reindexed from 1)		K9 G12 G50 G51 R55 G56 D70 G73 M74 M131 L133 F136 T138
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.4.22: UMP kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0005524 ATP binding
GO:0009041 UMP/dUMP kinase activity
GO:0016301 kinase activity
GO:0033862 UMP kinase activity
Biological Process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006225 UDP biosynthetic process
GO:0016310 phosphorylation
GO:0044210 'de novo' CTP biosynthetic process
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7bix, PDBe:7bix, PDBj:7bix
PDBsum7bix
PubMed35152545
UniProtP9WHK5|PYRH_MYCTU Uridylate kinase (Gene Name=pyrH)

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