6EJ1 | pdb_00006ej1

Crystal structure of KDM5B in complex with KDOPZ48a.

• PDB DOI: https://doi.org/10.2210/pdb6EJ1/pdb

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


• Deposited: 2017-09-19 Released: 2018-05-02 
• Deposition Author(s): Srikannathasan, V., Newman, J.A., Szykowska, A., Wright, M., Ruda, G.F., Vazquez-Rodriguez, S.A., Kupinska, K., Strain-Damerell, C., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A., Bountra, C., Oppermann, U., Huber, K., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.217 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Crystal structure of KDM5B in complex with KDOPZ48a.

srikannathasan, v.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.87 kDa 
• Atom Count: 3,933 
• Modeled Residue Count: 453 
• Deposited Residue Count: 459 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 5B,Lysine-specific demethylase 5B	A	459	Homo sapiens	Mutation(s): 0  Gene Names: KDM5B, JARID1B, PLU1, RBBP2H1 EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGL1 (Homo sapiens) Explore Q9UGL1  Go to UniProtKB:  Q9UGL1
PHAROS:  Q9UGL1 GTEx:  ENSG00000117139

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B7Q (Subject of Investigation/LOI)	H [auth A]	5-[1-[1-(2-chloranylethanoyl)piperidin-4-yl]pyrazol-4-yl]-7-oxidanylidene-6-propan-2-yl-4~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile C20 H22 Cl N7 O2 UFTLGLOWZBFFND-UHFFFAOYSA-N
DMS	E [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B7Q	BindingDB:  6EJ1	IC50: min: 65, max: 300 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.217 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.21	α = 90
b = 143.21	β = 90
c = 153.82	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Srikannathasan, V., Newman, J.A., Szykowska, A., Wright, M., Ruda, G.F., Vazquez-Rodriguez, S.A., Kupinska, K., Strain-Damerell, C., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A., Bountra, C., Oppermann, U., Huber, K., von Delft, F.

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary