6N4E

hPGDS complexed with a quinoline-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.206 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

The discovery of quinoline-3-carboxamides as hematopoietic prostaglandin D synthase (H-PGDS) inhibitors.

Deaton, D.N.Do, Y.Holt, J.Jeune, M.R.Kramer, H.F.Larkin, A.L.Orband-Miller, L.A.Peckham, G.E.Poole, C.Price, D.J.Schaller, L.T.Shen, Y.Shewchuk, L.M.Stewart, E.L.Stuart, J.D.Thomson, S.A.Ward, P.Wilson, J.W.Xu, T.Guss, J.H.Musetti, C.Rendina, A.R.Affleck, K.Anders, D.Hancock, A.P.Hobbs, H.Hodgson, S.T.Hutchinson, J.Leveridge, M.V.Nicholls, H.Smith, I.E.D.Somers, D.O.Sneddon, H.F.Uddin, S.Cleasby, A.Mortenson, P.N.Richardson, C.Saxty, G.

(2019) Bioorg Med Chem 27: 1456-1478

  • DOI: https://doi.org/10.1016/j.bmc.2019.02.017
  • Primary Citation of Related Structures:  
    6N4E, 6N69

  • PubMed Abstract: 

    With the goal of discovering more selective anti-inflammatory drugs, than COX inhibitors, to attenuate prostaglandin signaling, a fragment-based screen of hematopoietic prostaglandin D synthase was performed. The 76 crystallographic hits were sorted into similar groups, with the 3-cyano-quinoline 1a (FP IC 50  = 220,000 nM, LE = 0.43) being a potent member of the 6,6-fused heterocyclic cluster. Employing SAR insights gained from structural comparisons of other H-PGDS fragment binding mode clusters, the initial hit 1a was converted into the 70-fold more potent quinoline 1d (IC 50  = 3,100 nM, LE = 0.49). A systematic substitution of the amine moiety of 1d, utilizing structural information and array chemistry, with modifications to improve inhibitor stability, resulted in the identification of the 300-fold more active H-PGDS inhibitor tool compound 1bv (IC 50  = 9.9 nM, LE = 0.42). This selective inhibitor exhibited good murine pharmacokinetics, dose-dependently attenuated PGD 2 production in a mast cell degranulation assay and should be suitable to further explore H-PGDS biology.


  • Organizational Affiliation

    GlaxoSmithKline, 5 Moore Drive, P.O. Box 13398, Research Triangle Park, NC 27709, USA. Electronic address: david.n.deaton@gsk.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hematopoietic prostaglandin D synthase200Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KCD (Subject of Investigation/LOI)
Query on KCD

Download Ideal Coordinates CCD File 
C [auth A]7-(difluoromethoxy)-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]quinoline-3-carboxamide
C20 H24 F2 N2 O3
YRWMWDLEUYLURJ-SHTZXODSSA-N
GSH
Query on GSH

Download Ideal Coordinates CCD File 
B [auth A]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KCD BindingDB:  6N4E Kd: 0.5 (nM) from 1 assay(s)
IC50: 9.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.206 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.599α = 90
b = 72.76β = 90
c = 93.985γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
MOLREPphasing

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 KCDClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references