Structure of PDB 6apz Chain A Binding Site BS02

Receptor Information
>6apz Chain A (length=707) Species: 419947 (Mycobacterium tuberculosis H37Ra) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDRVSVGNLRIARVLYDFVNNEALPGTDIDPDSFWAGVDKVVADLTPQNQ
ALLNARDELQAQIDKWHRREPIDMDAYRQFLTEIGYLLPEPDDFTITTSG
VDAEITTTAGPQLVVPVLNARFALNAANARWGSLYDALYGTDVIPETDGA
EKGPTYNKVRGDKVIAYARKFLDDSVPLSSGSFGDATGFTVQDGQLVVAL
PDKSTGLANPGQFAGYTGAAESPTSVLLINHGLHIEILIDPESQVGTTDR
AGVKDVILESAITTIMDFEDSVAAVDAADKVLGYRNWLGLNKGDLAARVL
NRDRNYTAPGGGQFTLPGRSLMFVRNVGHLMTNDAIVDTDGSEVFEGIMD
ALFTGLIAIHGLKASDPLINSRTGSIYIVKPKMHGPAEVAFTCELFSRVE
DVLGLPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGFLDRTGDE
IHTSMEAGPMVRKGTMKSQPWILAYEDHNVDAGLAAGFSGRAQVGKGMWT
MTELMADMVETKIAQPRAGASTAWVPSPTAATLHALHYHQVDVAAVQQGL
AGKRRATIEQLLTIPLAKELAWAPDEIREEVDNNCQSILGYVVRWVDQGV
GASKVPDIHDVALMEDRATLRISSQLLANWLRHGVITSADVRASLERMAP
LVDRQNVAYRPMAPNFDDSIAFLAAQELILSGAQQPNGYTEPILHRRRRE
FKARAAE
Ligand information
Ligand IDBQ4
InChIInChI=1S/C10H8O5/c11-7-3-1-2-6(4-7)8(12)5-9(13)10(14)15/h1-5,11,13H,(H,14,15)/b9-5-
InChIKeyWWHSBYDKAHIVPP-UITAMQMPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(cc(c1)O)C(=O)C=C(C(=O)O)O
CACTVS 3.385OC(=O)C(O)=CC(=O)c1cccc(O)c1
OpenEye OEToolkits 2.0.6c1cc(cc(c1)O)C(=O)/C=C(/C(=O)O)\O
ACDLabs 12.01c1ccc(O)cc1C([C@H]=C(C(O)=O)O)=O
CACTVS 3.385OC(=O)\C(O)=C\C(=O)c1cccc(O)c1
FormulaC10 H8 O5
Name(2Z)-2-hydroxy-4-(3-hydroxyphenyl)-4-oxobut-2-enoic acid;
3-hydroxy-phenyldiketoacid
ChEMBL
DrugBank
ZINCZINC000379702115
PDB chain6apz 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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PDB6apz Anion-pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.
Resolution2.254 Å
Binding residue
(original residue number in PDB)		R339 G459 L461 D462 M515 W541 M631 D633
Binding residue
(residue number reindexed from 1)		R325 G442 L444 D445 M498 W524 M614 D616
Annotation score1
Binding affinityMOAD: ic50=0.15uM
PDBbind-CN: -logKd/Ki=6.82,IC50=0.15uM
Enzymatic activity
Catalytic site (original residue number in PDB) D271 E273 R339 E434 D462 D633
Catalytic site (residue number reindexed from 1) D267 E269 R325 E417 D445 D616
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:6apz, PDBe:6apz, PDBj:6apz
PDBsum6apz
PubMed30137983
UniProtP9WK17|MASZ_MYCTU Malate synthase G (Gene Name=glcB)

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