Structure of PDB 6dik Chain A Binding Site BS01

Receptor Information
>6dik Chain A (length=121) Species: 8726 (Bothrops jararacussu) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCC
YKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENL
GTYNKKYRYHLKPFCKKADPC
Ligand information
Ligand IDGKP
InChIInChI=1S/C22H18O12/c23-13-5-1-11(9-15(13)25)3-7-17(27)33-19(21(29)30)20(22(31)32)34-18(28)8-4-12-2-6-14(24)16(26)10-12/h1-10,19-20,23-26H,(H,29,30)(H,31,32)/b7-3+,8-4+/t19-,20-/m1/s1
InChIKeyYDDGKXBLOXEEMN-IABMMNSOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(c(cc1C=CC(=O)OC(C(C(=O)O)OC(=O)C=Cc2ccc(c(c2)O)O)C(=O)O)O)O
OpenEye OEToolkits 2.0.6c1c(cc(c(c1)O)O)/C=C/C(=O)O[C@@H](C(=O)O)[C@@H](OC(=O)/C=C/c2cc(c(cc2)O)O)C(=O)O
CACTVS 3.385OC(=O)[CH](OC(=O)C=Cc1ccc(O)c(O)c1)[CH](OC(=O)C=Cc2ccc(O)c(O)c2)C(O)=O
ACDLabs 12.01c1c(cc(c(c1)O)O)[C@H]=CC(=O)OC(C(=O)O)C(OC([C@H]=[C@H]c2ccc(c(c2)O)O)=O)C(=O)O
CACTVS 3.385OC(=O)[C@H](OC(=O)\C=C\c1ccc(O)c(O)c1)[C@@H](OC(=O)/C=C/c2ccc(O)c(O)c2)C(O)=O
FormulaC22 H18 O12
Name(2R,3R)-2,3-bis{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}butanedioic acid
ChEMBLCHEMBL282731
DrugBank
ZINCZINC000004098726
PDB chain6dik Chain A Residue 201 [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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PDB6dik Structural basis of phospholipase A2-like myotoxin inhibition by chicoric acid, a novel potent inhibitor of ophidian toxins.
Resolution1.93 Å
Binding residue
(original residue number in PDB)		F3 G6 K7
Binding residue
(residue number reindexed from 1)		F3 G6 K7
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.07,Kd=8.47uM
Enzymatic activity
Catalytic site (original residue number in PDB) N28 G30 L32 H48 K49 Y52 Y73 D99
Catalytic site (residue number reindexed from 1) N27 G29 L31 H47 K48 Y51 Y64 D89
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004623 phospholipase A2 activity
GO:0005509 calcium ion binding
GO:0005543 phospholipid binding
GO:0008201 heparin binding
GO:0047498 calcium-dependent phospholipase A2 activity
GO:0090729 toxin activity
Biological Process
GO:0006644 phospholipid metabolic process
GO:0016042 lipid catabolic process
GO:0035821 modulation of process of another organism
GO:0042130 negative regulation of T cell proliferation
GO:0042742 defense response to bacterium
GO:0050482 arachidonate secretion
Cellular Component
GO:0005576 extracellular region

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Biological Process
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Cellular Component
External links
PDB RCSB:6dik, PDBe:6dik, PDBj:6dik
PDBsum6dik
PubMed30251662
UniProtQ90249|PA2H1_BOTJR Basic phospholipase A2 homolog bothropstoxin-I

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