Structure of PDB 6w58 Chain B Binding Site BS01

Receptor Information
>6w58 Chain B (length=199) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGK
IPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMS
CFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWAD
FYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL
Ligand information
Ligand IDSWS
InChIInChI=1S/C21H28N4O2/c1-21(2,27)16-4-6-17(7-5-16)24-20(26)15-10-14-12-23-19(25-8-3-9-25)11-18(14)22-13-15/h10-13,16-17,27H,3-9H2,1-2H3,(H,24,26)/t16-,17-
InChIKeyYBOJDFGHCNHNOW-QAQDUYKDSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)(O)[C@H]1CC[C@@H](CC1)NC(=O)c2cnc3cc(ncc3c2)N4CCC4
CACTVS 3.385CC(C)(O)[CH]1CC[CH](CC1)NC(=O)c2cnc3cc(ncc3c2)N4CCC4
OpenEye OEToolkits 2.0.7CC(C)(C1CCC(CC1)NC(=O)c2cc3cnc(cc3nc2)N4CCC4)O
FormulaC21 H28 N4 O2
Name7-(azetidin-1-yl)-~{N}-[4-(2-oxidanylpropan-2-yl)cyclohexyl]-1,6-naphthyridine-3-carboxamide
ChEMBLCHEMBL5279860
DrugBank
ZINC
PDB chain6w58 Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6w58 The exploration of aza-quinolines as hematopoietic prostaglandin D synthase (H-PGDS) inhibitors with low brain exposure.
Resolution2.395 Å
Binding residue
(original residue number in PDB)		G13 R14 M99 W104 A105 Y152 I155
Binding residue
(residue number reindexed from 1)		G13 R14 M99 W104 A105 Y152 I155
Annotation score1
Binding affinityMOAD: ic50=3.9nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y8 R14 R19 W104
Catalytic site (residue number reindexed from 1) Y8 R14 R19 W104
Enzyme Commision number 2.5.1.18: glutathione transferase.
5.3.99.2: prostaglandin-D synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004364 glutathione transferase activity
GO:0004667 prostaglandin-D synthase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0016853 isomerase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0001516 prostaglandin biosynthetic process
GO:0006693 prostaglandin metabolic process
GO:0007165 signal transduction
GO:0007626 locomotory behavior
GO:0009624 response to nematode
GO:0010269 response to selenium ion
GO:2000255 negative regulation of male germ cell proliferation
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6w58, PDBe:6w58, PDBj:6w58
PDBsum6w58
PubMed33059303
UniProtO60760|HPGDS_HUMAN Hematopoietic prostaglandin D synthase (Gene Name=HPGDS)

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