7DYU | pdb_00007dyu

Human JMJD5 in complex with MN and 5-((4-phenylbutyl)amino)pyridine-2,4-dicarboxylic acid.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.195 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

5-Substituted Pyridine-2,4-dicarboxylate Derivatives Have Potential for Selective Inhibition of Human Jumonji-C Domain-Containing Protein 5.

Brewitz, L.Nakashima, Y.Piasecka, S.K.Salah, E.Fletcher, S.C.Tumber, A.Corner, T.P.Kennedy, T.J.Fiorini, G.Thalhammer, A.Christensen, K.E.Coleman, M.L.Schofield, C.J.

(2023) J Med Chem 66: 10849-10865

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01114
  • Primary Citation of Related Structures:  
    7DYT, 7DYU, 7DYV, 7DYW, 7DYX

  • PubMed Abstract: 

    Jumonji-C domain-containing protein 5 (JMJD5) is a 2-oxoglutarate (2OG)-dependent oxygenase that plays important roles in development, circadian rhythm, and cancer through unclear mechanisms. JMJD5 has been reported to have activity as a histone protease, as an N ε -methyl lysine demethylase, and as an arginine residue hydroxylase. Small-molecule JMJD5-selective inhibitors will be useful for investigating its (patho)physiological roles. Following the observation that the broad-spectrum 2OG oxygenase inhibitor pyridine-2,4-dicarboxylic acid (2,4-PDCA) is a 2OG-competing JMJD5 inhibitor, we report that 5-aminoalkyl-substituted 2,4-PDCA derivatives are potent JMJD5 inhibitors manifesting selectivity for JMJD5 over other human 2OG oxygenases. Crystallographic analyses with five inhibitors imply induced fit binding and reveal that the 2,4-PDCA C5 substituent orients into the JMJD5 substrate-binding pocket. Cellular studies indicate that the lead compounds display similar phenotypes as reported for clinically observed JMJD5 variants, which have a reduced catalytic activity compared to wild-type JMJD5.


  • Organizational Affiliation
    • Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional peptidase and arginyl-hydroxylase JMJD5235Homo sapiensMutation(s): 0 
Gene Names: KDM8JMJD5
EC: 1.14.11 (PDB Primary Data), 3.4 (PDB Primary Data), 1.14.11.73 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N371 (Homo sapiens)
Explore Q8N371 
Go to UniProtKB:  Q8N371
PHAROS:  Q8N371
GTEx:  ENSG00000155666 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N371
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.372α = 90
b = 64.564β = 90
c = 78.486γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-29
    Changes: Refinement description
  • Version 1.3: 2023-12-06
    Changes: Database references