6ZTC

CRYSTAL STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE IN COMPLEX WITH FRAGMENT 1A AT 1.84A RESOLUTION.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: other
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QPNClick on this verticalbar to view details

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: christie.a.schulte@gsk.com.


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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
QPN (Subject of Investigation/LOI)
Query on QPN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
1-[1-(3-fluorophenyl)-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-5-yl]propan-1-one
C15 H16 F N3 O
PBPQRCMCEYVHIP-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
QPN BindingDB:  6ZTC IC50: 2800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.071α = 90
b = 68.163β = 96.7
c = 68.517γ = 90
Software Package:
Software NamePurpose
MOSFLMdata processing
SCALAdata scaling
TRUNCATEdata reduction
REFMACphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QPNClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2021-07-28 
  • Deposition Author(s): Somers, D.O.

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description