Structure of PDB 7tin Chain B Binding Site BS02

Receptor Information
>7tin Chain B (length=556) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GNHKAALTKQVFTFASELYAYGVREVVISPGSRSTPLALAFEAHPNIKTW
IHPDERSAAFFAVGLIKGSERPVAILCTSGTAAANYTPAIAESQISRIPL
IVLTSDRPHELRSVGAPQAINQVNMFNNYVSYEFDMPIADDSKETINAIY
YQMQIASQYLYGPHKGPIHFNLPFRDPLTPDLNATELLTSEMKILPHYQK
SIDASALRHILNKKKGLIIVGDMQHQEVDQILTYSTIYDLPILADPLSHL
RKFDHPNVICTYDLLFRSGLDLNVDFVIRVGKPVISKKLNQWLKKTDAFQ
ILVQNNDKIDVFPIAPDISYEISANDFFRSLMEDTTINRVSWLEKWQCLE
KKGRKEIKCYLEQATDESAFVGELIKKTSEKDALFISNSMPIRDVDNLLL
NKNIDVYANRGANGIDGIVSTALGMAVHKRITLLIGDLSFYHDMNGLLMS
KLNNIQMNIVLLNNDGGGIFSYLPQKESATDYFERLFGTPTGLDFEYTAK
LYQFDFKRFNSVSEFKNATLLSETSTIYELITNREDNFKQHQILYQKLSE
MIHDTL
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 chain7tin Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7tin Allosteric inhibition of Staphylococcus aureus MenD by 1,4-dihydroxy naphthoic acid: a feedback inhibition mechanism of the menaquinone biosynthesis pathway.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		S390 M391 I416 D417 G437 D438 L439 S440 N465 G467 G469 I470
Binding residue
(residue number reindexed from 1)		S389 M390 I415 D416 G436 D437 L438 S439 N464 G466 G468 I469
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: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:7tin, PDBe:7tin, PDBj:7tin
PDBsum7tin
PubMed36633276
UniProtQ2FZL7|MEND_STAA8 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

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