5V18 | pdb_00005v18

Structure of PHD2 in complex with 1,2,4-Triazolo-[1,5-a]pyridine

• PDB DOI: https://doi.org/10.2210/pdb5V18/pdb

• Classification: Oxidoreductase/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.235 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

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

• PubMed: 28594552 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b00352
• Primary Citation Related Structures: 
  5V18, 5V1B


• 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-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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.16 kDa 
• Atom Count: 1,765 
• Modeled Residue Count: 215 
• Deposited Residue Count: 239 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egl nine homolog 1	A	239	Homo sapiens	Mutation(s): 0  Gene Names: EGLN1, C1orf12, PNAS-118, PNAS-137 EC: 1.14.11.29
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZT9 (Homo sapiens) Explore Q9GZT9  Go to UniProtKB:  Q9GZT9
PHAROS:  Q9GZT9 GTEx:  ENSG00000135766

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8UY	D [auth A]	4-([1,2,4]triazolo[1,5-a]pyridin-5-yl)benzonitrile C13 H8 N4 DEYMFBHALUHGST-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE2	E [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.235 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.528	α = 90
b = 72.528	β = 90
c = 45.642	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations