5KE2

Crystal structure of SETDB1 Tudor domain in complex with inhibitor XST06472A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of SETDB1 Tudor domain in complex with inhibitor xst06472a

Iqbal, A.Mader, P.Dong, A.Dobrovetsky, E.Walker, J.R.Bountra, C.Arrowsmith, C.H.Edwards, A.M.Brown, P.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SETDB1213Homo sapiensMutation(s): 0 
Gene Names: SETDB1KIAA0067KMT1E
UniProt & NIH Common Fund Data Resources
Find proteins for Q15047 (Homo sapiens)
Explore Q15047 
Go to UniProtKB:  Q15047
PHAROS:  Q15047
GTEx:  ENSG00000143379 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15047
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6S4
Query on 6S4

Download Ideal Coordinates CCD File 
B [auth A](3~{S})-~{N}-~{tert}-butyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide
C14 H20 N2 O
DMJXRYSGXCLCFP-LBPRGKRZSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth A]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.816α = 90
b = 63.891β = 90
c = 69.793γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description