4JZR

Structure of Prolyl Hydroxylase Domain-containing Protein (PHD) with Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Novel complex crystal structure of prolyl hydroxylase domain-containing protein 2 (PHD2): 2,8-Diazaspiro[4.5]decan-1-ones as potent, orally bioavailable PHD2 inhibitors

Deng, G.Zhao, B.Ma, Y.Xu, Q.Wang, H.Yang, L.Zhang, Q.Guo, T.B.Zhang, W.Jiao, Y.Cai, X.Zhang, J.Liu, H.Guan, X.Lu, H.Xiang, J.Elliott, J.D.Lin, X.Ren, F.

(2013) Bioorg.Med.Chem. 21: 6349-6358

  • DOI: 10.1016/j.bmc.2013.08.046

  • PubMed Abstract: 
  • We have discovered a novel complex crystal structure of the PHD2 enzyme with its inhibitor, the 2,8-diazaspiro[4.5]decan-1-one analogue 4b. The widely reported salt bridge between Arg383 of the enzyme and its inhibitors in all complex structures publ ...

    We have discovered a novel complex crystal structure of the PHD2 enzyme with its inhibitor, the 2,8-diazaspiro[4.5]decan-1-one analogue 4b. The widely reported salt bridge between Arg383 of the enzyme and its inhibitors in all complex structures published thus far was not observed in our case. In our complex structure compound 4b forms several novel interactions with the enzyme, which include a hydrogen bond with Arg322, a π-cation interaction with Arg322, a π-π stacking with Trp389, and a π-π stacking with His313. Guided by the structural information, SAR studies were performed on the 2,8-diazaspiro[4.5]decan-1-one series leading to the discovery of compound 9p with high potency and good oral pharmacokinetic profile in mice.


    Organizational Affiliation

    Research and Development, GlaxoSmithKline Pharmaceuticals, 898 Halei Road, Zhangjiang Hi-tech Park, Pudong, Shanghai 201203, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Egl nine homolog 1
A
216Homo sapiensMutation(s): 0 
Gene Names: EGLN1 (C1orf12)
EC: 1.14.11.29
Find proteins for Q9GZT9 (Homo sapiens)
Go to Gene View: EGLN1
Go to UniProtKB:  Q9GZT9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4JR
Query on 4JR

Download SDF File 
Download CCD File 
A
2-(biphenyl-4-yl)-8-[(1-methyl-1H-imidazol-2-yl)methyl]-2,8-diazaspiro[4.5]decan-1-one
C25 H28 N4 O
QFZKAEGCEQQJEP-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4JRIC50: 16 nM (99) BINDINGDB
4JRIC50: 15.8 nM BINDINGMOAD
4JRIC50: 15.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.231 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 111.455α = 90.00
b = 111.455β = 90.00
c = 39.974γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
Blu-Icedata collection
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-04-03 
  • Released Date: 2013-10-30 
  • Deposition Author(s): Ma, Y., Yang, L.

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release