5FJK

Crystal structure of human JMJD2C catalytic domain in complex 6-ethyl- 5-methyl-7-oxo-4,7-dihydropyrazolo(1,5-a)pyrimidine-3-carbonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

wwPDB Validation 3D Report Full Report



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
349Homo sapiensMutation(s): 0 
Gene Names: KDM4CGASC1JHDM3CJMJD2CKIAA0780
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt)
Find proteins for Q9H3R0 (Homo sapiens)
Go to UniProtKB:  Q9H3R0
NIH Common Fund Data Resources
PHAROS  Q9H3R0
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EM6
Query on EM6

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A
6-ethyl-5-methyl-7-oxidanylidene-1H-pyrazolo[1,5-a]pyrimidine-3-carbonitrile
C10 H10 N4 O
PJIRQIUNBLUWJK-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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

Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.9α = 90
b = 91.27β = 90
c = 98.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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