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 

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Ligand Structure Quality Assessment 


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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:  
    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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hematopoietic prostaglandin D synthaseA, B200Homo sapiensMutation(s): 0 
Gene Names: HPGDS, GSTS, PGDS, PTGDS2
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60760
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VH4 (Subject of Investigation/LOI)
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

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Ligand Structure Quality Assessment 


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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