Structure of PDB 6dlj Chain A Binding Site BS02

Receptor Information
>6dlj Chain A (length=704) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDRVSVGNLRIARVLYDFVNNEALPGTDIDPDSFWAGVDKVVADLTPQNQ
ALLNARDELQAQIDKWHRRIDMDAYRQFLTEIGYLLPEPDDFTITTSGVD
AEITTTAGPQLVVPVLNARFALNAANARWGSLYDALYGTDVIPETDGAEK
GPTYNKVRGDKVIAYARKFLDDSVPLSSGSFGDATGFTVQDGQLVVALPD
KSTGLANPGQFAGYTGAAESPTSVLLINHGLHIEILIDPESQVGTTDRAG
VKDVILESAITTIMDFEDSVAAVDAADKVLGYRNWLGLNKGDLAARVLNR
DRNYTAPGGGQFTLPGRSLMFVRNVGHLMTNDAIVDTDGSEVFEGIMDAL
FTGLIAIHGLKASDLINSRTGSIYIVKPKMHGPAEVAFTCELFSRVEDVL
GLPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGFLDRTGDEIHT
SMEAGPMVRKGTMKSQPWILAYEDHNVDAGLAAGFSGRAQVGKGMWTMTE
LMADMVETKIAQPRAGASTAWVPSPTAATLHALHYHQVDVAAVQQGLAGK
RRATIEQLLTIPLAKELAWAPDEIREEVDNNCQSILGYVVRWVDQGVGCS
KVPDIHDVALMEDRATLRISSQLLANWLRHGVITSADVRASLERMAPLVD
RQNAAYRPMAPNFDDSIAFLAAQELILSGAQQPNGYTEPILHRRRREFKA
RAAE
Ligand information
Ligand IDGXM
InChIInChI=1S/C10H7NO6/c12-8(5-9(13)10(14)15)6-3-1-2-4-7(6)11(16)17/h1-5,13H,(H,14,15)/b9-5-
InChIKeyAPXXDBVLXHIFHL-UITAMQMPSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1(ccccc1C([C@H]=C(C(O)=O)O)=O)[N+]([O-])=O
CACTVS 3.385OC(=O)C(O)=CC(=O)c1ccccc1[N+]([O-])=O
OpenEye OEToolkits 2.0.6c1ccc(c(c1)C(=O)C=C(C(=O)O)O)[N+](=O)[O-]
OpenEye OEToolkits 2.0.6c1ccc(c(c1)C(=O)/C=C(/C(=O)O)\O)[N+](=O)[O-]
CACTVS 3.385OC(=O)\C(O)=C\C(=O)c1ccccc1[N+]([O-])=O
FormulaC10 H7 N O6
Name(2Z)-2-hydroxy-4-(2-nitrophenyl)-4-oxobut-2-enoic acid
ChEMBLCHEMBL1829212
DrugBank
ZINCZINC000101981294
PDB chain6dlj Chain A Residue 803 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6dlj Anion-pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.
Resolution2.604 Å
Binding residue
(original residue number in PDB)		V118 R339 E434 G459 F460 L461 D462 W541 M631 D633
Binding residue
(residue number reindexed from 1)		V112 R323 E414 G439 F440 L441 D442 W521 M611 D613
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.55,IC50=2.8uM
Enzymatic activity
Catalytic site (original residue number in PDB) D271 E273 R339 E434 D462 D633
Catalytic site (residue number reindexed from 1) D265 E267 R323 E414 D442 D613
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:6dlj, PDBe:6dlj, PDBj:6dlj
PDBsum6dlj
PubMed30137983
UniProtP9WK17|MASZ_MYCTU Malate synthase G (Gene Name=glcB)

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