5FZC

Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 4,5-dihydronaphtho(1,2-b)thiophene-2- carboxylicacid (N11181a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Maybridge Fragment 4,5-Dihydronaphtho(1,2-B)Thiophene-2-Carboxylicacid (N11181A) (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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC DEMETHYLASE 5B
A
479Homo sapiensMutation(s): 0 
Gene Names: KDM5B (JARID1B, PLU1, RBBP2H1)
EC: 1.14.11.-
Find proteins for Q9UGL1 (Homo sapiens)
Go to Gene View: KDM5B
Go to UniProtKB:  Q9UGL1
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
D8S
Query on D8S

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Download CCD File 
A
benzo[g][1]benzothiole-2-carboxylic acid
C13 H8 O2 S
KRSFUJUZIQCOHU-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.192 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 143.350α = 90.00
b = 143.350β = 90.00
c = 154.000γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
DIMPLEphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references, Structure summary