5V1B

Structure of PHD1 in complex with 1,2,4-Triazolo-[1,5-a]pyridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

1,2,4-Triazolo-[1,5-a]pyridine HIF Prolylhydroxylase Domain-1 (PHD-1) Inhibitors With a Novel Monodentate Binding Interaction.

Ahmed, S.Ayscough, A.Barker, G.R.Canning, H.E.Davenport, R.Downham, R.Harrison, D.Jenkins, K.Kinsella, N.Livermore, D.G.Wright, S.Ivetac, A.D.Skene, R.Wilkens, S.J.Webster, N.A.Hendrick, A.G.

(2017) J Med Chem 60: 5663-5672

  • DOI: 10.1021/acs.jmedchem.7b00352
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Herein we describe the identification of 4-{[1,2,4]triazolo[1,5-a]pyridin-5-yl}benzonitrile-based inhibitors of the hypoxia-inducible factor prolylhydroxylase domain-1 (PHD-1) enzyme. These inhibitors were shown to possess a novel binding mode by X-r ...

    Herein we describe the identification of 4-{[1,2,4]triazolo[1,5-a]pyridin-5-yl}benzonitrile-based inhibitors of the hypoxia-inducible factor prolylhydroxylase domain-1 (PHD-1) enzyme. These inhibitors were shown to possess a novel binding mode by X-ray crystallography, in which the triazolo N1 atom coordinates in a hitherto unreported monodentate interaction with the active site Fe 2+ ion, while the benzonitrile group accepts a hydrogen-bonding interaction from the side chain residue of Asn315. Further optimization led to potent PHD-1 inhibitors with good physicochemical and pharmacokinetic properties.


    Organizational Affiliation

    Department of Computational Sciences and Crystallography, Takeda California Inc. , 10410 Science Center Dr., San Diego, California 92121, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Egl nine homolog 2A240Homo sapiensMutation(s): 0 
Gene Names: EGLN2EIT6
EC: 1.14.11.29 (PDB Primary Data), 1.14.11 (UniProt)
Find proteins for Q96KS0 (Homo sapiens)
Explore Q96KS0 
Go to UniProtKB:  Q96KS0
NIH Common Fund Data Resources
PHAROS  Q96KS0
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8UY
Query on 8UY

Download CCD File 
A
4-([1,2,4]triazolo[1,5-a]pyridin-5-yl)benzonitrile
C13 H8 N4
DEYMFBHALUHGST-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8UYIC50:  34   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.717α = 90
b = 112.082β = 90
c = 66.223γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2017-03-01 
  • Released Date: 2017-06-21 
  • Deposition Author(s): Skene, R.J.

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references