Structure of PDB 2jla Chain D Binding Site BS02

Receptor Information
>2jla Chain D (length=556) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSVSAFNRRWAAVILEALTRHGVRHICIAPGSRSTPLTLAAAENSAFIHH
THFDERGLGHLALGLAKVSKQPVAVIVTSGTAVANLYPALIEAGLTGEKL
ILLTADRPPELIDCGANQAIRQPGMFASHPTHSISLPRPTQDIPARWLVS
TIDHALGTLHAGGVHINCPFAEPLYGEMDDTGLSWQQRLGDWWQDDKPWL
REAPRLESEKQRDWFFWRQKRGVVVAGRMSAEEGKKVALWAQTLGWPLIG
DVLSQTGQPLPCADLWLGNAKATSELQQAQIVVQLGSSLTGKRLLQWQAS
CEPEEYWIVDDIEGRLDPAHHRGRRLIANIADWLELHPAEKRQPWCVEIP
RLAEQAMQAVIARRDAFGEAQLAHRICDYLPEQGQLFVGNSLVVRLIDAL
SQLPAGYPVYSNRGASGIDGLLSTAAGVQRASGKPTLAIVGDLSALYDLN
ALALLRQVSAPLVLIVVNNNGGQIFSLLPTPQSERERFYLMPQNVHFEHA
AAMFELKYHRPQNWQELETAFADAWRTPTTTVIEMVVNDTDGAQTLQQLL
AQVSHL
Ligand information
Ligand IDTPP
InChIInChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKeyAYEKOFBPNLCAJY-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H19 N4 O7 P2 S
NameTHIAMINE DIPHOSPHATE
ChEMBLCHEMBL1236376
DrugBank
ZINCZINC000008215517
PDB chain2jla Chain D Residue 1557 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2jla Specificity and Reactivity in Menaquinone Biosynthesis: The Structure of Escherichia Coli Mend (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase).
Resolution2.81 Å
Binding residue
(original residue number in PDB)		S391 L392 I418 D419 G441 D442 L443 S444 Y447 N469 G471 G472 Q473 I474
Binding residue
(residue number reindexed from 1)		S391 L392 I418 D419 G441 D442 L443 S444 Y447 N469 G471 G472 Q473 I474
Annotation score1
Enzymatic activity
Enzyme Commision number 2.2.1.9: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0016740 transferase activity
GO:0030145 manganese ion binding
GO:0030976 thiamine pyrophosphate binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0070204 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity
Biological Process
GO:0009234 menaquinone biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2jla, PDBe:2jla, PDBj:2jla
PDBsum2jla
PubMed18983854
UniProtP17109|MEND_ECOLI 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

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