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

• PDB DOI: https://doi.org/10.2210/pdb7DYQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-01-22 Released: 2022-01-26 
• Deposition Author(s): Wang, T., Yang, L.

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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 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.37 kDa 
• Atom Count: 2,980 
• Modelled Residue Count: 330 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4D	A	330	Homo sapiens	Mutation(s): 0  Gene Names: KDM4D, JHDM3D, JMJD2D 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HR0 (Subject of Investigation/LOI)	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	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

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 = 71.635	α = 90
b = 71.635	β = 90
c = 151.486	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Wang, T., Yang, L.

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description