Structure of PDB 3u8d Chain A Binding Site BS01

Receptor Information
>3u8d Chain A (length=124) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCC
YKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFAR
NKTTYNKKYQYYSNKHCRGSTPRC
Ligand information
Ligand IDU8D
InChIInChI=1S/C22H27N2O5P/c1-2-20-19(14-22(23)25)18-13-17(29-11-6-12-30(26,27)28)9-10-21(18)24(20)15-16-7-4-3-5-8-16/h3-5,7-10,13H,2,6,11-12,14-15H2,1H3,(H2,23,25)(H2,26,27,28)
InChIKeyOPWQYOUZRHDKBR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCc1n(Cc2ccccc2)c3ccc(OCCC[P](O)(O)=O)cc3c1CC(N)=O
OpenEye OEToolkits 1.7.2CCc1c(c2cc(ccc2n1Cc3ccccc3)OCCCP(=O)(O)O)CC(=O)N
ACDLabs 12.01O=P(O)(O)CCCOc1cc2c(cc1)n(c(c2CC(=O)N)CC)Cc3ccccc3
FormulaC22 H27 N2 O5 P
Name(3-{[3-(2-amino-2-oxoethyl)-1-benzyl-2-ethyl-1H-indol-5-yl]oxy}propyl)phosphonic acid
ChEMBLCHEMBL146186
DrugBank
ZINCZINC000001543374
PDB chain3u8d 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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PDB3u8d Selective Inhibition of Human Group IIA-secreted Phospholipase A2 (hGIIA) Signaling Reveals Arachidonic Acid Metabolism Is Associated with Colocalization of hGIIA to Vimentin in Rheumatoid Synoviocytes.
Resolution1.805 Å
Binding residue
(original residue number in PDB)		L2 F5 H6 Y21 C28 G29 G31 H47 D48 K62 F98
Binding residue
(residue number reindexed from 1)		L2 F5 H6 Y21 C28 G29 G31 H47 D48 K62 F98
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.33,IC50=0.47uM
BindingDB: IC50=470nM
Enzymatic activity
Catalytic site (original residue number in PDB) H27 G29 G31 H47 D48 Y51 Y66 D91
Catalytic site (residue number reindexed from 1) H27 G29 G31 H47 D48 Y51 Y66 D91
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
Biological Process
GO:0006629 lipid metabolic process
GO:0006644 phospholipid metabolic process
GO:0006954 inflammatory response
GO:0010744 positive regulation of macrophage derived foam cell differentiation
GO:0016042 lipid catabolic process
GO:0031640 killing of cells of another organism
GO:0034374 low-density lipoprotein particle remodeling
GO:0036335 intestinal stem cell homeostasis
GO:0042130 negative regulation of T cell proliferation
GO:0042742 defense response to bacterium
GO:0046337 phosphatidylethanolamine metabolic process
GO:0046470 phosphatidylcholine metabolic process
GO:0046473 phosphatidic acid metabolic process
GO:0050482 arachidonate secretion
GO:0050729 positive regulation of inflammatory response
GO:0050830 defense response to Gram-positive bacterium
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:1902563 regulation of neutrophil activation
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005886 plasma membrane
GO:0030141 secretory granule
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3u8d, PDBe:3u8d, PDBj:3u8d
PDBsum3u8d
PubMed23482564
UniProtP14555|PA2GA_HUMAN Phospholipase A2, membrane associated (Gene Name=PLA2G2A)

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