Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 56.57 kDa 
• Atom Count: 3898 
• Residue Count: 455 
• Unique protein chains: 1

5FUN

Crystal structure of human JARID1B in complex with GSK467

• DOI: 10.2210/pdb5FUN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-01-28 Released: 2016-04-13 
• Deposition Author(s): Srikannathasan, V., Johansson, C., Gileadi, C., Kopec, J., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Brennan, P., Oppermann, U.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.

Johansson, C., Velupillai, S., Tumber, A., Szykowska, A., Hookway, E.S., Nowak, R.P., Strain-Damerell, C., Gileadi, C., Philpott, M., Burgess-Brown, N., Wu, N., Kopec, J., Nuzzi, A., Steuber, H., Egner, U., Badock, V., Munro, S., Lathangue, N.B., Westaway, S., Brown, J., Athanasou, N., Prinjha, R., Brennan, P.E., Oppermann, U.

(2016) Nat Chem Biol 12: 539

• PubMed: 27214403 
• DOI: 10.1038/nchembio.2087
• Primary Citation of Related Structures:  
  5A1F, 5A3W, 5A3P, 5A3T, 5FUN, 5FUP, 5FV3, 5FWJ, 4UF0, 5FPV


• PubMed Abstract: 
  

Members of the KDM5 (also known as JARID1) family are 2-oxoglutarate- and Fe(2+)-dependent oxygenases that act as histone H3K4 demethylases, thereby regulating cell proliferation and stem cell self-renewal and differentiation. Here we report crystal structures of the catalytic core of the human KDM5B enzyme in complex with three inhibitor chemotypes. These scaffolds exploit several aspects of the KDM5 active site, and their selectivity profiles reflect their hybrid features with respect to the KDM4 and KDM6 families. Whereas GSK-J1, a previously identified KDM6 inhibitor, showed about sevenfold less inhibitory activity toward KDM5B than toward KDM6 proteins, KDM5-C49 displayed 25-100-fold selectivity between KDM5B and KDM6B. The cell-permeable derivative KDM5-C70 had an antiproliferative effect in myeloma cells, leading to genome-wide elevation of H3K4me3 levels. The selective inhibitor GSK467 exploited unique binding modes, but it lacked cellular potency in the myeloma system. Taken together, these structural leads deliver multiple starting points for further rational and selective inhibitor design.

---

Organizational Affiliation: 

Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 5B	A	481	Homo sapiens	Mutation(s): 0  Gene Names: KDM5B, JARID1B, PLU1, RBBP2H1 EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
Find proteins for Q9UGL1 (Homo sapiens) Explore Q9UGL1  Go to UniProtKB:  Q9UGL1
NIH Common Fund Data Resources
PHAROS:  Q9UGL1 GTEx:  ENSG00000117139

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GZA	A	2-[(1-benzyl-1H-pyrazol-4-yl)oxy]pyrido[3,4-d]pyrimidin-4(3H)-one C17 H13 N5 O2 ZTYRLXUTLYBVHH-UHFFFAOYSA-N
EPE	A	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GZA	IC50:  26   nM  BindingDB
GZA	Ki:  10   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.842	α = 90
b = 142.842	β = 90
c = 152.011	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-01-28 
• Released Date: 2016-04-13 
Deposition Author(s): Srikannathasan, V., Johansson, C., Gileadi, C., Kopec, J., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Brennan, P., Oppermann, U.

Revision History 

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2016-05-25
  Changes: Database references
• Version 1.2: 2016-06-01
  Changes: Database references
• Version 1.3: 2016-06-29
  Changes: Database references