4K11

The structure of 1NA in complex with Src T338G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The structure of 1NA in complex with Src T338G

Eck, M.J.Yun, C.H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase SrcA448Homo sapiensMutation(s): 1 
Gene Names: SRCSRC1
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P12931 (Homo sapiens)
Explore P12931 
Go to UniProtKB:  P12931
PHAROS:  P12931
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0J9 (Subject of Investigation/LOI)
Query on 0J9

Download Ideal Coordinates CCD File 
B [auth A]1-tert-butyl-3-(naphthalen-1-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C19 H19 N5
XSHQBIXMLULFEV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
AL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
0J9 BindingDB:  4K11 IC50: min: 340, max: 1300 (nM) from 2 assay(s)
PTR BindingDB:  4K11 -TΔS: -1.81e+1 (kJ/mol) from 1 assay(s)
ΔG: -2.14e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.96α = 90
b = 72.72β = 90
c = 171.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2013-04-04 
  • Released Date: 2014-04-09 
  • Deposition Author(s): Eck, M.J., Yun, C.H.

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description