5NV2

Human DNMT3B PWWP domain in complex with N-isopropyl-1,5-dimethylhexylamine (Metron S)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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 UniProtKB:  Q9UBC3
NIH Common Fund Data Resources
PHAROS  Q9UBC3
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9AE
Query on 9AE

Download CCD File 
A, B
(2~{S})-6-methyl-~{N}-propan-2-yl-heptan-2-amine
C11 H25 N
NKGYBXHAQAKSSG-NSHDSACASA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.63α = 90
b = 74.63β = 90
c = 156.67γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



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
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection