5AIV

Complex of human hematopoietic prostagandin D2 synthase (hH-PGDS) in complex with an active site inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of Indole Inhibitors of Human Hematopoietic Prostaglandin D2 Synthase (Hh-Pgds).

Edfeldt, F.Even, J.Lepisto, M.Ward, A.Petersen, J.Wissler, L.Rohman, M.Sivars, U.Svensson, K.Perry, M.Feierberg, I.Zhou, X.H.Hansson, T.Narjes, F.

(2015) Bioorg Med Chem Lett 25: 2496

  • DOI: https://doi.org/10.1016/j.bmcl.2015.04.065
  • Primary Citation of Related Structures:  
    5AIS, 5AIV, 5AIX

  • PubMed Abstract: 

    Human H-PGDS has shown promise as a potential target for anti-allergic and anti-inflammatory drugs. Here we describe the discovery of a novel class of indole inhibitors, identified through focused screening of 42,000 compounds and evaluated using a series of hit validation assays that included fluorescence polarization binding, 1D NMR, ITC and chromogenic enzymatic assays. Compounds with low nanomolar potency, favorable physico-chemical properties and inhibitory activity in human mast cells have been identified. In addition, our studies suggest that the active site of hH-PGDS can accommodate larger structural diversity than previously thought, such as the introduction of polar groups in the inner part of the binding pocket.


  • Organizational Affiliation

    Discovery Sciences, Innovative Medicines, AstraZeneca R&D, 431 83 Molndal, Sweden. Electronic address: Fredrik.Edfeldt@astrazeneca.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
A, B, C, D
199Homo sapiensMutation(s): 0 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C],
N [auth D]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
M1W
Query on M1W

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
M [auth D]
3-(1H-indol-4-yl)-N-(3-methoxypropyl)-1,2,4-oxadiazole-5-carboxamide
C15 H16 N4 O3
BPSPJIVDNLKGAJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
L [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
M1W BindingDB:  5AIV Kd: 650 (nM) from 1 assay(s)
IC50: min: 170, max: 2900 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.02α = 90
b = 124.02β = 90
c = 106.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other