4ASK

CRYSTAL STRUCTURE OF JMJD3 WITH GSK-J1

Structural Biology Knowledgebase: 4ASK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.165

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4ASK

Classification: OXIDOREDUCTASE

Total Structure Weight: 117129.33

Macromolecule Entities
Molecule Chains Length Organism Details
LYSINE-SPECIFIC DEMETHYLASE 6B A, B 510 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: CATALYTIC AND ZBD DOMAIN
Gene Name(s): KDM6B Gene View JMJD3 KIAA0346

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
K0I
Query on K0I

A, B 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro- 3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid
3-((6-(4,5-dihydro-1H-benzo[d]azepin-3(2H)- yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid (Synonym)
C22 H23 N5 O2
AVZCPICCWKMZDT-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CO
Query on CO

A, B COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
K0I N/A in BindingDB
N/A in BindingMoad
IC50: 60 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.165
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.36 α = 85.98
b = 65.55 β = 67.69
c = 77.39 γ = 68.42

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-01
  • Released Date: 2012-07-25
  • Deposition author(s): Chung, C., Mosley, J., Liddle, J.

Revision History

  • 2012-08-29
    Type: Citation | Details: JRNL