Structure of PDB 3s9i Chain A Binding Site BS01

Receptor Information
>3s9i Chain A (length=714) 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
LRVLNRDRNYTAPGGGQFTLPGRSLMFVRNVGHLMTNDAIVDTDGSEVFE
GIMDALFTGLIAIHGLKASDGPLINSRTGSIYIVKPKMHGPAEVAFTCEL
FSRVEDVLGLPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGFLD
RTGDEIHTSMEAGPMVRKGTMKSQPWILAYEDHNVDAGLAAGFSGRAQVG
KGMWTMTELMADMVETKIAQPRAGASTAWVPSPTAATLHALHYHQVDVAA
VQQGLAGKRRATIEQLLTIPLAKELAWAPDEIREEVDNNCQSILGYVVRW
VDQGVGASKVPDIHDVALMEDRATLRISSQLLANWLRHGVITSADVRASL
ERMAPLVDRQNADVAYRPMAPNFDDSIAFLAAQELILSGAQQPNGYTEPI
LHRRRREFKARAAE
Ligand information
Ligand IDXI7
InChIInChI=1S/C10H8O4/c11-8(6-9(12)10(13)14)7-4-2-1-3-5-7/h1-5H,6H2,(H,13,14)
InChIKeyJGKFWCXVYCDKDU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(c1ccccc1)CC(=O)C(=O)O
CACTVS 3.352OC(=O)C(=O)CC(=O)c1ccccc1
OpenEye OEToolkits 1.6.1c1ccc(cc1)C(=O)CC(=O)C(=O)O
FormulaC10 H8 O4
Name2-4-DIOXO-4-PHENYLBUTANOIC ACID
ChEMBLCHEMBL19332
DrugBank
ZINCZINC000012375863
PDB chain3s9i Chain A Residue 742 [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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PDB3s9i Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		R339 E434 G459 L461 D462 M515 W541 D633
Binding residue
(residue number reindexed from 1)		R329 E422 G447 L449 D450 M503 W529 D621
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.70,IC50=2.0uM
Enzymatic activity
Catalytic site (original residue number in PDB) D271 E273 R339 E434 D462 D633
Catalytic site (residue number reindexed from 1) D270 E272 R329 E422 D450 D621
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:3s9i, PDBe:3s9i, PDBj:3s9i
PDBsum3s9i
PubMed23261599
UniProtP9WK17|MASZ_MYCTU Malate synthase G (Gene Name=glcB)

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