5LW9

Crystal structure of human JARID1B in complex with S40563a

• PDB DOI: https://doi.org/10.2210/pdb5LW9/pdb

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


• Deposited: 2016-09-15 Released: 2016-09-28 
• Deposition Author(s): Srikannathasan, V., Le Bihan, Y.V., Szykowska, A., Johansson, C., Gileadi, C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Oppermann, U., Huber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.218 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Crystal structure of human JARID1B in complex with S40563a

srikannathasan, v.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.46 kDa 
• Atom Count: 3,854 
• Modelled Residue Count: 456 
• Deposited Residue Count: 481 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 5B,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)
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
5UJ	I [auth A]	8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one C23 H22 Cl2 N6 O RLRGPZGIQMEBLC-UHFFFAOYSA-N
DMS	F [auth A], G [auth A], H [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]	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
5UJ	BindingDB:  5LW9	IC50: 14 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.218 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.96	α = 90
b = 142.96	β = 90
c = 152.47	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Srikannathasan, V., Le Bihan, Y.V., Szykowska, A., Johansson, C., Gileadi, C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Oppermann, U., Huber, K.

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description