5NRV

Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3BA [auth D],
B [auth A]
150Homo sapiensMutation(s): 0 
Gene Names: DNMT3B
EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBC3 (Homo sapiens)
Explore Q9UBC3 
Go to UniProtKB:  Q9UBC3
PHAROS:  Q9UBC3
GTEx:  ENSG00000088305 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBC3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
96K
Query on 96K

Download Ideal Coordinates CCD File 
C [auth D],
J [auth A]
6-dipropylamino-1-hexanol
C12 H27 N O
NGLYVCQIAOHIJE-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D
E [auth D]
F [auth D]
G [auth D]
H [auth D]
D,
E [auth D],
F [auth D],
G [auth D],
H [auth D],
I [auth D],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.55α = 90
b = 73.55β = 90
c = 155.3γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description