Structure of PDB 1kpm Chain A Binding Site BS01

Receptor Information
>1kpm Chain A (length=121) Species: 97228 (Daboia russelii pulchella) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCC
YGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNL
NTYSKKYMLYPDFLCKGELKC
Ligand information
Ligand IDVIT
InChIInChI=1S/C29H50O2/c1-20(2)12-9-13-21(3)14-10-15-22(4)16-11-18-29(8)19-17-26-25(7)27(30)23(5)24(6)28(26)31-29/h20-22,30H,9-19H2,1-8H3/t21-,22-,29-/m0/s1
InChIKeyGVJHHUAWPYXKBD-SYZUXVNWSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)CCC[C@H](C)CCC[C@H](C)CCC[C@@]1(C)CCc2c(C)c(O)c(C)c(C)c2O1
OpenEye OEToolkits 1.5.0Cc1c(c2c(c(c1O)C)CCC(O2)(C)CCCC(C)CCCC(C)CCCC(C)C)C
OpenEye OEToolkits 1.5.0Cc1c(c2c(c(c1O)C)CC[C@](O2)(C)CCC[C@@H](C)CCC[C@@H](C)CCCC(C)C)C
ACDLabs 10.04Oc2c(c(c1OC(CCc1c2C)(C)CCCC(C)CCCC(C)CCCC(C)C)C)C
CACTVS 3.341CC(C)CCC[CH](C)CCC[CH](C)CCC[C]1(C)CCc2c(C)c(O)c(C)c(C)c2O1
FormulaC29 H50 O2
NameVITAMIN E;
2,5,7,8-TETRAMETHYL-2-(4,8,12-TRIMETHYLTRIDECYL)-6-CHROMANOL
ChEMBL
DrugBank
ZINCZINC000002083220
PDB chain1kpm Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1kpm First Structural Evidence of a Specific Inhibition of Phospholipase A2 by alpha-Tocopherol (Vitamin E) and its Implications in Inflammation: Crystal Structure of the Complex Formed Between Phospholipase A2 and alpha-Tocopherol at 1.8 A Resolution
Resolution1.8 Å
Binding residue
(original residue number in PDB)		L2 L3 G6 K7 A18 I19 Y22 S23 C45 H48 D49
Binding residue
(residue number reindexed from 1)		L2 L3 G6 K7 A17 I18 Y21 S22 C44 H47 D48
Annotation score1
Binding affinityMOAD: Ki=1.59uM
PDBbind-CN: -logKd/Ki=5.80,Ki=1.59uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y28 G30 G32 H48 D49 Y52 Y73 D99
Catalytic site (residue number reindexed from 1) Y27 G29 G31 H47 D48 Y51 Y64 D89
Enzyme Commision number 3.1.1.4: phospholipase A2.
Gene Ontology
Molecular Function
GO:0004623 phospholipase A2 activity
GO:0005509 calcium ion binding
GO:0005543 phospholipid binding
GO:0016787 hydrolase activity
GO:0046872 metal ion 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:0050482 arachidonate secretion
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1kpm, PDBe:1kpm, PDBj:1kpm
PDBsum1kpm
PubMed12079380
UniProtP59071|PA2B8_DABRR Basic phospholipase A2 VRV-PL-VIIIa

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