Structure of PDB 5ywx Chain B Binding Site BS02

Receptor Information
>5ywx Chain B (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 B Residue 203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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 R14 Q36 M99 W104 A105
Binding residue
(residue number reindexed from 1)		M10 R13 Q35 M98 W103 A104
Annotation score1
Binding affinityMOAD: 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
View graph for
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)

[Back to BioLiP]