Structure of PDB 5ess Chain D Binding Site BS01

Receptor Information
>5ess Chain D (length=542) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHV
RIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLI
VLSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAEDAPERTSALNA
TWRSATCRVLAAATGARTANAGPVHFDIPLREPTPPGRPAGKPWTYTPPV
TFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPL
ALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQ
ATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAV
SHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAI
GAALAYEGAHERTGSPDSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSL
TIVVSNDNGGGIFELLEQGDPRFSDVSSRIFGTPHDVDVGALCRAYHVES
RQIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL
Ligand information
Ligand IDTOG
InChIInChI=1S/C16H24N4O10P2S/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/h7,21H,3-6,8H2,1-2H3,(H,22,23)(H,27,28)(H2,17,18,19)(H2,24,25,26)
InChIKeyVGWJMSNWDAXPBE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C-](O)CCC(O)=O)c(N)n1
OpenEye OEToolkits 2.0.4Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O
FormulaC16 H24 N4 O10 P2 S
Name4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3 -ium-2-yl]-4-oxidanyl-butanoic acid;
ThDP and decarboxylated 2-oxoglutarate adduct, covalent intermediate I, carboanion form
ChEMBL
DrugBank
ZINC
PDB chain5ess 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5ess Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		S377 N378 R381 R399 A402 G403 I404 D405 G439 D440 L441 T442 D469 G471 G472 G473 I474 F475
Binding residue
(residue number reindexed from 1)		S365 N366 R369 R387 A390 G391 I392 D393 G427 D428 L429 T430 D457 G459 G460 G461 I462 F463
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C26 E55
Catalytic site (residue number reindexed from 1) C25 E54
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: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
Cellular Component
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ess, PDBe:5ess, PDBj:5ess
PDBsum5ess
PubMed27291649
UniProtP9WK11|MEND_MYCTU 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

[Back to BioLiP]