6W8H | pdb_00006w8h

H-PGDS complexed with inhibitor 1Y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.239 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6W8H

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

The exploration of aza-quinolines as hematopoietic prostaglandin D synthase (H-PGDS) inhibitors with low brain exposure.

Cadilla, R.Deaton, D.N.Do, Y.Elkins, P.A.Ennulat, D.Guss, J.H.Holt, J.Jeune, M.R.King, A.G.Klapwijk, J.C.Kramer, H.F.Kramer, N.J.Laffan, S.B.Masuria, P.I.McDougal, A.V.Mortenson, P.N.Musetti, C.Peckham, G.E.Pietrak, B.L.Poole, C.Price, D.J.Rendina, A.R.Sati, G.Saxty, G.Shearer, B.G.Shewchuk, L.M.Sneddon, H.F.Stewart, E.L.Stuart, J.D.Thomas, D.N.Thomson, S.A.Ward, P.Wilson, J.W.Xu, T.Youngman, M.A.

(2020) Bioorg Med Chem 28: 115791-115791

  • DOI: https://doi.org/10.1016/j.bmc.2020.115791
  • Primary Citation Related Structures: 
    6W58, 6W8H

  • PubMed Abstract: 

    GlaxoSmithKline and Astex Pharmaceuticals recently disclosed the discovery of the potent H-PGDS inhibitor GSK2894631A 1a (IC 50  = 9.9 nM) as part of a fragment-based drug discovery collaboration with Astex Pharmaceuticals. This molecule exhibited good murine pharmacokinetics, allowing it to be utilized to explore H-PGDS pharmacology in vivo. Yet, with prolonged dosing at higher concentrations, 1a induced CNS toxicity. Looking to attenuate brain penetration in this series, aza-quinolines, were prepared with the intent of increasing polar surface area. Nitrogen substitutions at the 6- and 8-positions of the quinoline were discovered to be tolerated by the enzyme. Subsequent structure activity studies in these aza-quinoline scaffolds led to the identification of 1,8-naphthyridine 1y (IC 50  = 9.4 nM) as a potent peripherally restricted H-PGDS inhibitor. Compound 1y is efficacious in four in vivo inflammatory models and exhibits no CNS toxicity.


  • Organizational Affiliation
    • GlaxoSmithKline, 5 Moore Drive, P.O. Box 13398, Research Triangle Park, NC 27709, USA.

Macromolecule Content 

  • Total Structure Weight: 51.75 kDa 
  • Atom Count: 3,410 
  • Modeled Residue Count: 397 
  • Deposited Residue Count: 426 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hematopoietic prostaglandin D synthaseA,
B [auth C]
213Homo 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
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
TJG BindingDB:  6W8H Kd: 0.24 (nM) from 1 assay(s)
IC50: 9.4 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.239 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.331α = 90
b = 67.197β = 96.88
c = 69.74γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description