7JR8

H-PDGS complexed with a 2-phenylimidazo[1,2-a]pyridine-6-carboxamide inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.115 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A knowledge-based, structural-aided discovery of a novel class of 2-phenylimidazo[1,2-a]pyridine-6-carboxamide H-PGDS inhibitors.

Schulte, C.A.Deaton, D.N.Diaz, E.Do, Y.Gampe, R.T.Guss, J.H.Hancock, A.P.Hobbs, H.Hodgson, S.T.Holt, J.Jeune, M.R.Kahler, K.M.Kramer, H.F.Le, J.Mortenson, P.N.Musetti, C.Nolte, R.T.Orband-Miller, L.A.Peckham, G.E.Petrov, K.G.Pietrak, B.L.Poole, C.Price, D.J.Saxty, G.Shillings, A.Smalley Jr., T.L.Somers, D.O.Stewart, E.L.Stuart, J.D.Thomson, S.A.

(2021) Bioorg Med Chem Lett 47: 128113-128113

  • DOI: https://doi.org/10.1016/j.bmcl.2021.128113
  • Primary Citation of Related Structures:  
    6ZTC, 7JR6, 7JR8

  • PubMed Abstract: 

    Through an internal virtual screen at GlaxoSmithKline a distinct class of 2-phenylimidazo[1,2-a]pyridine-6-carboxamide H-PGDS inhibitors were discovered. Careful evaluation of crystal structures and SAR led to a novel, potent, and orally active imidazopyridine inhibitor of H-PGDS, 20b. Herein, describes the identification of 2 classes of inhibitors, their syntheses, and their challenges.


  • Organizational Affiliation

    GlaxoSmithKline, 5 Moore Drive, P.O. Box 13398, Research Triangle Park, NC 27709, United States. Electronic address: [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hematopoietic prostaglandin D synthase
A, B
200Homo sapiensMutation(s): 0 
Gene Names: HPGDSGSTSPGDSPTGDS2
EC: 5.3.99.2 (PDB Primary Data), 2.5.1.18 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60760 (Homo sapiens)
Explore O60760 
Go to UniProtKB:  O60760
PHAROS:  O60760
GTEx:  ENSG00000163106 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60760
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VH7 (Subject of Investigation/LOI)
Query on VH7

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-2-phenylimidazo[1,2-a]pyridine-6-carboxamide
C23 H27 N3 O2
GOQZMCCBUBCPNK-WGSAOQKQSA-N
GSH
Query on GSH

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
M [auth B],
N [auth B],
O [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VH7 BindingDB:  7JR8 IC50: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.115 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.082α = 90
b = 93.489β = 105.519
c = 47.913γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references