Structure of PDB 1ayp Chain D Binding Site BS03

Receptor Information

>1ayp Chain D (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 ID

INB

InChI

InChI=1S/C26H54NO6PS/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-31-23-26(27-25(2)28)24-33-34(29,30)32-21-22-35-3/h26H,4-24H2,1-3H3,(H,27,28)(H,29,30)/t26-/m1/s1

InChIKey

ZULTVWFLRZJENJ-AREMUKBSSA-N

SMILES

Software	SMILES
CACTVS 3.341	CCCCCCCCCCCCCCCCCCOC[CH](CO[P](O)(=O)OCCSC)NC(C)=O
ACDLabs 10.04	O=P(OCC(NC(=O)C)COCCCCCCCCCCCCCCCCCC)(OCCSC)O
OpenEye OEToolkits 1.5.0	CCCCCCCCCCCCCCCCCCOCC(COP(=O)(O)OCCSC)NC(=O)C
OpenEye OEToolkits 1.5.0	CCCCCCCCCCCCCCCCCCOC[C@H](CO[P@@](=O)(O)OCCSC)NC(=O)C
CACTVS 3.341	CCCCCCCCCCCCCCCCCCOC[C@H](CO[P@](O)(=O)OCCSC)NC(C)=O

Formula

C26 H54 N O6 P S

Name

1-OCTADECYL-2-ACETAMIDO-2-DEOXY-SN-GLYCEROL-3-PHOSPHOETHYLMETHYL SULFIDE

PDB chain

1ayp Chain D Residue 204 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	1ayp A probe molecule composed of seventeen percent of total diffracting matter gives correct solutions in molecular replacement.
Resolution	2.57 Å
Binding residue (original residue number in PDB)	F5 A18 G22 G29 G31 C44 H47 D48 Y51 K52
Binding residue (residue number reindexed from 1)	F5 A18 G22 G29 G31 C44 H47 D48 Y51 K52
Annotation score	1

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:1ayp, PDBe:1ayp, PDBj:1ayp
PDBsum	1ayp
PubMed	15299314
UniProt	P14555\|PA2GA_HUMAN Phospholipase A2, membrane associated (Gene Name=PLA2G2A)

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