6FUL

Crystal structure of UTX complexed with 5-hydroxy-4-keto-1-methyl-picolinate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.649 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

In Silico Identification of JMJD3 Demethylase Inhibitors.

Esposito, C.Wiedmer, L.Caflisch, A.

(2018) J Chem Inf Model 58: 2151-2163

  • DOI: 10.1021/acs.jcim.8b00539
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the search for new demethylase inhibitors, we have developed a multistep protocol for in silico screening. Millions of poses generated by high-throughput docking or a 3D-pharmacophore search are first minimized by a classical force field and then ...

    In the search for new demethylase inhibitors, we have developed a multistep protocol for in silico screening. Millions of poses generated by high-throughput docking or a 3D-pharmacophore search are first minimized by a classical force field and then filtered by semiempirical quantum mechanical calculations of the interaction energy with a selected set of functional groups in the binding site. The final ranking includes solvation effects which are evaluated in the continuum dielectric approximation (finite-difference Poisson equation). Application of the multistep protocol to JMJD3 jumonji demethylase has resulted in a dozen low-micromolar inhibitors belonging to five different chemical classes. We have solved the crystal structure of JMJD3 inhibitor 8 in the complex with UTX (a demethylase in the same subfamily as JMJD3) which validates the predicted binding mode. Compound 8 is a promising candidate for future optimization as it has a favorable ligand efficiency of 0.32 kcal/mol per nonhydrogen atom.


    Organizational Affiliation

    Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zurich , Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 6A
A
531Homo sapiensMutation(s): 0 
Gene Names: KDM6A (UTX)
EC: 1.14.11.-
Find proteins for O15550 (Homo sapiens)
Go to Gene View: KDM6A
Go to UniProtKB:  O15550
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PG0
Query on PG0

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Download CCD File 
A
2-(2-METHOXYETHOXY)ETHANOL
PEG 6000
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
E7Z
Query on E7Z

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Download CCD File 
A
1-methyl-5-oxidanyl-4-oxidanylidene-pyridine-2-carboxylic acid
C7 H7 N O4
XWHROGRDGWNCHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.649 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 79.181α = 90.00
b = 82.801β = 90.00
c = 93.156γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references, Structure summary