Structure of PDB 5wzt Chain A Binding Site BS02

Receptor Information
>5wzt Chain A (length=123) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLVQFGVMIEKMTGKSALQYNDYGCYCGIGGSHWPVDQTDWCCHAHDCCY
GRLEKLGCEPKLEKYLFSVSERGIFCAGRTTCQRLTCECDKRAALCFRRN
LGTYNRKYAHYPNKLCTGPTPPC
Ligand information
Ligand ID7W6
InChIInChI=1S/C20H17BrN2O5/c1-11-17(19(26)20(22)27)18-14(6-3-7-15(18)28-10-16(24)25)23(11)9-12-4-2-5-13(21)8-12/h2-8H,9-10H2,1H3,(H2,22,27)(H,24,25)
InChIKeyZWWWBZCFNLMLRT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1c(c2c(n1Cc3cccc(c3)Br)cccc2OCC(=O)O)C(=O)C(=O)N
CACTVS 3.385Cc1n(Cc2cccc(Br)c2)c3cccc(OCC(O)=O)c3c1C(=O)C(N)=O
FormulaC20 H17 Br N2 O5
Name2-[1-[(3-bromophenyl)methyl]-2-methyl-3-oxamoyl-indol-4-yl]oxyethanoic acid
ChEMBL
DrugBank
ZINC
PDB chain5wzt Chain A Residue 204 [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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PDB5wzt Structural basis for functional selectivity and ligand recognition revealed by crystal structures of human secreted phospholipase A2 group IIE
Resolution2.4 Å
Binding residue
(original residue number in PDB)		L2 F5 G6 I9 A17 Y20 N21 C27 G28 I29 C43 H46 D47 F97
Binding residue
(residue number reindexed from 1)		L2 F5 G6 I9 A17 Y20 N21 C27 G28 I29 C43 H46 D47 F97
Annotation score1
Binding affinityMOAD: ic50=0.22uM
PDBbind-CN: -logKd/Ki=6.66,IC50=0.22uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y26 G28 G30 H46 D47 Y50 Y65 D90
Catalytic site (residue number reindexed from 1) Y26 G28 G30 H46 D47 Y50 Y65 D90
Enzyme Commision number 3.1.1.4: phospholipase A2.
Gene Ontology
Molecular Function
GO:0004623 phospholipase A2 activity
GO:0005509 calcium ion binding
GO:0005515 protein 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:0016042 lipid catabolic process
GO:0034374 low-density lipoprotein particle remodeling
GO:0042130 negative regulation of T cell proliferation
GO:0046470 phosphatidylcholine metabolic process
GO:0046471 phosphatidylglycerol metabolic process
GO:0050482 arachidonate secretion
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5wzt, PDBe:5wzt, PDBj:5wzt
PDBsum5wzt
PubMed28883454
UniProtQ9NZK7|PA2GE_HUMAN Group IIE secretory phospholipase A2 (Gene Name=PLA2G2E)

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