5FZB

Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 4-Pyridylthiourea (N06275b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Maybridge Fragment 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc -Diamond I04-1 Fragment Screening)

Nowak, R.Krojer, T.Johansson, C.Kupinska, K.Szykowska, A.Pearce, N.Talon, R.Collins, P.Gileadi, C.Strain-Damerell, C.Burgess-Brown, N.A.Arrowsmith, C.H.Bountra, C.Edwards, A.M.von Delft, F.Brennan, P.E.Oppermann, U.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LYSINE-SPECIFIC DEMETHYLASE 5B479Homo sapiensMutation(s): 0 
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UGL1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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G [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
YS6
Query on YS6

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Q [auth A]1-pyridin-4-ylthiourea
C6 H7 N3 S
HLOFIQOOOSRNFY-UHFFFAOYSA-N
PO4
Query on PO4

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R [auth A],
S [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
DMS
Query on DMS

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D [auth A],
E [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

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B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

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F [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

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P [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.41α = 90
b = 143.41β = 90
c = 153.37γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
DIMPLEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references, Structure summary
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description