7DYQ

Crystal structure of histone lysine demethylase 4D (KDM4D) in complex with the inhibitor 5-hydroxy-2-methylpyrazolo[1,5-a]pyrido[3,2-e]pyrimidine-3-carbonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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 histone lysine demethylase 4D (KDM4D) in complex with the inhibitor 5-hydroxy-2-methylpyrazolo[1,5-a]pyrido[3,2-e]pyrimidine-3-carbonitrile

Wang, T.Yang, L.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine-specific demethylase 4D330Homo sapiensMutation(s): 0 
Gene Names: KDM4DJHDM3DJMJD2D
EC: 1.14.11.66
UniProt & NIH Common Fund Data Resources
Find proteins for Q6B0I6 (Homo sapiens)
Explore Q6B0I6 
Go to UniProtKB:  Q6B0I6
PHAROS:  Q6B0I6
GTEx:  ENSG00000186280 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6B0I6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HR0 (Subject of Investigation/LOI)
Query on HR0

Download Ideal Coordinates CCD File 
B [auth A]5-hydroxy-2-methylpyrazolo[1,5-a]pyrido[3,2-e]pyrimidine-3-carbonitrile
C11 H7 N5 O
FIRSAIIBSBCBTF-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
HR0 BindingDB:  7DYQ IC50: 410 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.635α = 90
b = 71.635β = 90
c = 151.486γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary