Structure of PDB 6axb Chain A Binding Site BS02

Receptor Information
>6axb Chain A (length=715) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDRVSVGNLRIARVLYDFVNNEALPGTDIDPDSFWAGVDKVVADLTPQNQ
ALLNARDELQAQIDKWHRRRVIEPIDMDAYRQFLTEIGYLLPEPDDFTIT
TSGVDAEITTTAGPQLVVPVLNARFALNAANARWGSLYDALYGTDVIPET
DGAEKGPTYNKVRGDKVIAYARKFLDDSVPLSSGSFGDATGFTVQDGQLV
VALPDKSTGLANPGQFAGYTGAAESPTSVLLINHGLHIEILIDPESQVGT
TDRAGVKDVILESAITTIMDFEDSVAAVDAADKVLGYRNWLGLNKGDLAA
ALRVLNRDRNYTAPGGGQFTLPGRSLMFVRNVGHLMTNDAIVDTDGSEVF
EGIMDALFTGLIAIHGLKASDGPLINSRTGSIYIVKPKMHGPAEVAFTCE
LFSRVEDVLGLPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGFL
DRTGDEIHTSMEAGPMVRKGTMKSQPWILAYEDHNVDAGLAAGFSGRAQV
GKGMWTMTELMADMVETKIAQPRAGASTAWVPSPTAATLHALHYHQVDVA
AVQQGLAGKRRATIEQLLTIPLAKELAWAPDEIREEVDNNCQSILGYVVR
WVDQGVGASKVPDIHDVALMEDRATLRISSQLLANWLRHGVITSADVRAS
LERMAPLVDRQNADVAYRPMAPNFDDSIAFLAAQELILSGAQQPNGYTEP
ILHRRRREFKARAAE
Ligand information
Ligand IDC0V
InChIInChI=1S/C14H10O4/c15-12(8-13(16)14(17)18)11-6-5-9-3-1-2-4-10(9)7-11/h1-8,16H,(H,17,18)/b13-8-
InChIKeyMXSFSJCCMVMMQM-JYRVWZFOSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c2cc1ccccc1cc2C([C@H]=C(C(O)=O)O)=O
CACTVS 3.385OC(=O)C(O)=CC(=O)c1ccc2ccccc2c1
OpenEye OEToolkits 2.0.6c1ccc2cc(ccc2c1)C(=O)/C=C(/C(=O)O)\O
OpenEye OEToolkits 2.0.6c1ccc2cc(ccc2c1)C(=O)C=C(C(=O)O)O
CACTVS 3.385OC(=O)\C(O)=C\C(=O)c1ccc2ccccc2c1
FormulaC14 H10 O4
Name(2Z)-2-hydroxy-4-(naphthalen-2-yl)-4-oxobut-2-enoic acid
ChEMBL
DrugBank
ZINCZINC000167822210
PDB chain6axb Chain A Residue 802 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6axb Anion-pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		V118 R339 E434 G459 L461 D462 M515 W541 M631 D633
Binding residue
(residue number reindexed from 1)		V117 R330 E423 G448 L450 D451 M504 W530 M620 D622
Annotation score1
Binding affinityMOAD: ic50=0.5uM
PDBbind-CN: -logKd/Ki=6.30,IC50=0.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) D271 E273 R339 E434 D462 D633
Catalytic site (residue number reindexed from 1) D270 E272 R330 E423 D451 D622
Enzyme Commision number 2.3.3.9: malate synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0001968 fibronectin binding
GO:0003824 catalytic activity
GO:0004474 malate synthase activity
GO:0005515 protein binding
GO:0005518 collagen binding
GO:0016740 transferase activity
GO:0042803 protein homodimerization activity
GO:0043236 laminin binding
GO:0046810 host cell extracellular matrix binding
GO:0046872 metal ion binding
GO:0120225 coenzyme A binding
Biological Process
GO:0006097 glyoxylate cycle
GO:0006099 tricarboxylic acid cycle
GO:0009436 glyoxylate catabolic process
GO:0015936 coenzyme A metabolic process
GO:0044406 adhesion of symbiont to host
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall
GO:0009986 cell surface
GO:0042603 capsule

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6axb, PDBe:6axb, PDBj:6axb
PDBsum6axb
PubMed30137983
UniProtP9WK17|MASZ_MYCTU Malate synthase G (Gene Name=glcB)

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