5AIX | pdb_00005aix

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.343 (Depositor), 0.324 (DCC) 
  • R-Value Work: 
    0.256 (Depositor) 
  • R-Value Observed: 
    0.261 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5AIX

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 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.

Macromolecule Content 

  • Total Structure Weight: 94.96 kDa 
  • Atom Count: 6,749 
  • Modeled Residue Count: 792 
  • Deposited Residue Count: 796 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KRX

Query on KRX



Download:Ideal Coordinates CCD File
G [auth B],
I [auth C]
6-(3-methoxyphenyl)-N-[1-(2,2,2-trifluoroethyl)piperidin-4-yl]pyridine-3-carboxamide
C20 H22 F3 N3 O2
KJXMFUFGGQJXRP-UHFFFAOYSA-N
GSH

Query on GSH



Download:Ideal Coordinates CCD File
F [auth B],
H [auth C]
Glutathione
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A],
J [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.343 (Depositor), 0.324 (DCC) 
  • R-Value Work:  0.256 (Depositor) 
  • R-Value Observed: 0.261 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.228α = 90
b = 122.228β = 90
c = 106.023γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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