5AIX

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 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.bmcl.2015.04.065
  • Primary Citation of Related Structures:  
    5AIV, 5AIX, 5AIS

  • 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 s ...

    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

    Respiratory, Inflammation and Autoimmunity, Innovative Medicines, AstraZeneca R&D, 431 83 Molndal, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEMATOPOIETIC PROSTAGLANDIN D SYNTHASEABCD199Homo sapiensMutation(s): 0 
Gene Names: HPGDSGSTSPGDSPTGDS2
EC: 5.3.99.2 (PDB Primary Data), 2.5.1.18 (PDB Primary Data)
Find proteins for O60760 (Homo sapiens)
Explore O60760 
Go to UniProtKB:  O60760
NIH Common Fund Data Resources
PHAROS  O60760
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KRX
Query on KRX

Download CCD File 
B, C
6-(3-methoxyphenyl)-N-[1-(2,2,2-trifluoroethyl)piperidin-4-yl]pyridine-3-carboxamide
C20 H22 F3 N3 O2
KJXMFUFGGQJXRP-UHFFFAOYSA-N
 Ligand Interaction
GSH
Query on GSH

Download CCD File 
B, C
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KRXIC50:  60   nM  BindingDB
KRXKd:  12   nM  BindingDB
KRXIC50:  210   nM  BindingDB
KRXEC50:  130   nM  BindingDB
KRXKd:  170   nM  Binding MOAD
KRXKd:  44   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.343 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.261 
  • 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



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references