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

Literature

Macromolecules
Sequence Display for 4JZR

Classification: OXIDOREDUCTASE

Total Structure Weight: 24751.79

Macromolecule Entities
Molecule Chains Length Organism Details
Egl nine homolog 1 A 216 Homo sapiens EC#: 1.14.11.29 IUBMB
Fragment: UNP residues 189-399
Gene Name(s): EGLN1 Gene View C1orf12 PNAS-118 PNAS-137
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
4JR
Query on 4JR

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 Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
4JR IC50: 16 nM (99) BindingDB

IC50: 15.8 nM  BindingMOAD
IC50: 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 = 111.46 α = 90.00
b = 111.46 β = 90.00
c = 39.97 γ = 120.00

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

No revisions since initial release