Structure of PDB 6dko Chain A Binding Site BS02

Receptor Information
>6dko Chain A (length=716) 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
AVFLRVLNRDRNYTAPGGGQFTLPGRSLMFVRNVGHLMTNDAIVDTDGSE
VFEGIMDALFTGLIAIHGLKASGPLINSRTGSIYIVKPKMHGPAEVAFTC
ELFSRVEDVLGLPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGF
LDRTGDEIHTSMEAGPMVRKGTMKSQPWILAYEDHNVDAGLAAGFSGRAQ
VGKGMWTMTELMADMVETKIAQPRAGASTAWVPSPTAATLHALHYHQVDV
AAVQQGLAGKRRATIEQLLTIPLAKEAWAPDEIREEVDNNCQSILGYVVR
WVDQGVGASKVPDIHDVALMEDRATLRISSQLLANWLRHGVITSADVRAS
LERMAPLVDRQNAGDVAYRPMAPNFDDSIAFLAAQELILSGAQQPNGYTE
PILHRRRREFKARAAE
Ligand information
Ligand IDGXG
InChIInChI=1S/C10H6F2O4/c11-5-2-1-3-6(12)9(5)7(13)4-8(14)10(15)16/h1-3H,4H2,(H,15,16)
InChIKeyXDJANDPQWKAGNO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(c(c(c1)F)C(=O)CC(=O)C(=O)O)F
CACTVS 3.385OC(=O)C(=O)CC(=O)c1c(F)cccc1F
ACDLabs 12.01c1(cccc(c1C(CC(C(O)=O)=O)=O)F)F
FormulaC10 H6 F2 O4
Name4-(2,6-difluorophenyl)-2,4-dioxobutanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6dko Chain A Residue 804 [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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PDB6dko Anion-pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.
Resolution1.556 Å
Binding residue
(original residue number in PDB)		R339 G459 L461 D462 M515 W541 M631 D633
Binding residue
(residue number reindexed from 1)		R332 G449 L451 D452 M505 W531 M620 D622
Annotation score1
Binding affinityMOAD: ic50=1.6uM
PDBbind-CN: -logKd/Ki=5.80,IC50=1.6uM
Enzymatic activity
Catalytic site (original residue number in PDB) D271 E273 R339 E434 D462 D633
Catalytic site (residue number reindexed from 1) D270 E272 R332 E424 D452 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
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Cellular Component
External links
PDB RCSB:6dko, PDBe:6dko, PDBj:6dko
PDBsum6dko
PubMed30137983
UniProtP9WK17|MASZ_MYCTU Malate synthase G (Gene Name=glcB)

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