5FJH

Crystal structure of human JMJD2C catalytic domain in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino) -2-oxoethyl)amino)methyl)isonicotinic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structures of Human Jmjd2C Catalytic Domain Bound to Inhibitors

Cecatiello, V.Pasqualato, S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC DEMETHYLASE 4C
A, B
349Homo sapiensMutation(s): 0 
Gene Names: KDM4C (GASC1, JHDM3C, JMJD2C, KIAA0780)
EC: 1.14.11.-
Find proteins for Q9H3R0 (Homo sapiens)
Go to Gene View: KDM4C
Go to UniProtKB:  Q9H3R0
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MMK
Query on MMK

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A, B
2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid
C15 H22 N4 O3
RTKGUAPXWDCFNW-BQYQJAHWSA-N
 Ligand Interaction
CL
Query on CL

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A, B
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
NI
Query on NI

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A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.185 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 89.240α = 90.00
b = 95.920β = 90.00
c = 100.430γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release