6EIY | pdb_00006eiy

Crystal structure of KDM5B in complex with KDOPZ000034a.

• PDB DOI: https://doi.org/10.2210/pdb6EIY/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: 2.15 Å
• R-Value Free: 
  0.215 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of KDM5B in complex with KDOPZ000034a.

srikannathasan, v.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.14 kDa 
• Atom Count: 3,916 
• Modeled Residue Count: 456 
• Deposited Residue Count: 461 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 5B,Lysine-specific demethylase 5B	A	461	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
B6W (Subject of Investigation/LOI)	K [auth A]	2-chloranyl-~{N}-[2-[4-(3-cyano-7-oxidanylidene-6-propan-2-yl-4~{H}-pyrazolo[1,5-a]pyrimidin-5-yl)pyrazol-1-yl]ethyl]ethanamide C17 H18 Cl N7 O2 TUVMHEGGYLIJHD-UHFFFAOYSA-N
DMS	G [auth A], H [auth A], I [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	C [auth A], J [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B6W	BindingDB:  6EIY	IC50: min: 7, max: 530 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.215 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.38	α = 90
b = 142.38	β = 90
c = 152.17	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: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary