Structure of PDB 5ywx Chain A Binding Site BS02

Receptor Information
>5ywx Chain A (length=198) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKI
PILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSC
FPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADF
YWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL
Ligand information
Ligand ID93C
InChIInChI=1S/C20H17N5O2/c26-18-5-3-11-25(18)16-8-6-15(7-9-16)24-20(27)14-12-22-19(23-13-14)17-4-1-2-10-21-17/h1-2,4,6-10,12-13H,3,5,11H2,(H,24,27)
InChIKeyMYYXEGDPWAHVAZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1ccnc(c1)c4ncc(C(=O)Nc3ccc(N2C(=O)CCC2)cc3)cn4
CACTVS 3.385O=C1CCCN1c2ccc(NC(=O)c3cnc(nc3)c4ccccn4)cc2
OpenEye OEToolkits 2.0.6c1ccnc(c1)c2ncc(cn2)C(=O)Nc3ccc(cc3)N4CCCC4=O
FormulaC20 H17 N5 O2
NameN-[4-(2-oxopyrrolidin-1-yl)phenyl]-2-(pyridin-2-yl)pyrimidine-5-carboxamide
ChEMBLCHEMBL4238290
DrugBank
ZINC
PDB chain5ywx Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ywx Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies.
Resolution1.74 Å
Binding residue
(original residue number in PDB)		M11 G13 R14 Q36 M99 W104 Y152
Binding residue
(residue number reindexed from 1)		M10 G12 R13 Q35 M98 W103 Y151
Annotation score1
Binding affinityMOAD: Kd=0.14nM
PDBbind-CN: -logKd/Ki=9.85,Kd=0.14nM
BindingDB: Kd=0.140000nM
Enzymatic activity
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
View graph for
Cellular Component
External links
PDB RCSB:5ywx, PDBe:5ywx, PDBj:5ywx
PDBsum5ywx
PubMed30121213
UniProtO60760|HPGDS_HUMAN Hematopoietic prostaglandin D synthase (Gene Name=HPGDS)

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