5NV0

Human DNMT3B PWWP domain in complex with 4-(dipropylamino)butyronitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.399 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Targeting PWWP domain of DNA methyltransferase 3B for epigenetic cancer therapy: Identification and structural characterization of new potential protein-protein interaction inhibitors

Rondelet, G.Dal Maso, T.Maniquet, A.Themans, Q.Wouters, J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA (cytosine-5)-methyltransferase 3B
A, B
150Homo sapiensMutation(s): 0 
Gene Names: DNMT3B
EC: 2.1.1.37
Find proteins for Q9UBC3 (Homo sapiens)
Go to Gene View: DNMT3B
Go to UniProtKB:  Q9UBC3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
9AH
Query on 9AH

Download SDF File 
Download CCD File 
A, B
4-(dipropylamino)butanenitrile
C10 H20 N2
FLJPZKPNJVGMHO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.399 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.260α = 90.00
b = 74.260β = 90.00
c = 159.100γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
F.R.S._FNRS_TelevieBelgium7.4.532.15.F.

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2019-03-27
    Type: Data collection, Database references
  • Version 1.2: 2019-10-16
    Type: Data collection