7JR6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1016/j.bmcl.2021.128113
  • Primary Citation of Related Structures:  
    7JR8, 7JR6

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hematopoietic prostaglandin D synthaseA, B200Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VH4
Query on VH4

Download Ideal Coordinates CCD File 
D [auth A], I [auth B]1-(3-fluorophenyl)-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide
C22 H29 F N4 O2
APPNXGOPROLJQR-SAABIXHNSA-N
 Ligand Interaction
GSH
Query on GSH

Download Ideal Coordinates CCD File 
C [auth A], H [auth B]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], J [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.872α = 90
b = 67.997β = 96.831
c = 69.096γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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