Structure of PDB 5z2r Chain D Binding Site BS02

Receptor Information
>5z2r 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
RLAEQAMQAVIARRDAFGEAQLAHRICDYLPEQGQLFVGNSLVVKLIDAL
SQLPAGYPVYSNRGASGIDGLLSTAAGVQRASGKPTLAIVGDLSALYDLN
ALALLRQVSAPLVLIVVNNNGGQIFSLLPTPQSERERFYLMPQNVHFEHA
AAMFELKYHRPQNWQELETAFADAWRTPTTTVIEMVVNDTDGAQTLQQLL
AQVSHL
Ligand information
Ligand IDTD6
InChIInChI=1S/C16H26N4O10P2S/c1-9-13(5-6-29-32(27,28)30-31(24,25)26)33-16(12(21)3-4-14(22)23)20(9)8-11-7-18-10(2)19-15(11)17/h7,12,20-21H,3-6,8H2,1-2H3,(H,22,23)(H,27,28)(H2,17,18,19)(H2,24,25,26)/t12-/m0/s1
InChIKeyRWCNVMPVYGBSHH-LBPRGKRZSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[CH](O)CCC(O)=O)c(N)n1
OpenEye OEToolkits 1.7.6Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O
ACDLabs 12.01O=C(O)CCC(O)c1sc(c(n1Cc2cnc(nc2N)C)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.370Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@@H](O)CCC(O)=O)c(N)n1
OpenEye OEToolkits 1.7.6Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O
FormulaC16 H25 N4 O10 P2 S
Name(4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid
ChEMBL
DrugBank
ZINC
PDB chain5z2r Chain D Residue 601 [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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PDB5z2r Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		S391 L392 R413 I418 D419 G441 D442 L443 S444 N469 G471 G472 Q473 I474 F475
Binding residue
(residue number reindexed from 1)		S391 L392 R413 I418 D419 G441 D442 L443 S444 N469 G471 G472 Q473 I474 F475
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:5z2r, PDBe:5z2r, PDBj:5z2r
PDBsum5z2r
PubMed30341164
UniProtP17109|MEND_ECOLI 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

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