4ZOG

VX-680/MK-0457 binds to human ABL1 also in inactive DFG conformations.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

VX-680/MK-0457 binds also to human ABL1 with inactive DFG conformations.

Kyomuhendo, P.Narayanan, D.Engh, R.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase ABL1
A, B
283Homo sapiensMutation(s): 0 
Gene Names: ABL1ABLJTK7
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P00519 (Homo sapiens)
Explore P00519 
Go to UniProtKB:  P00519
PHAROS:  P00519
GTEx:  ENSG00000097007 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00519
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VX6
Query on VX6

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE
C23 H28 N8 O S
GCIKSSRWRFVXBI-UHFFFAOYSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
H [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
MXE
Query on MXE

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
2-METHOXYETHANOL
C3 H8 O2
XNWFRZJHXBZDAG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VX6 BindingDB:  4ZOG Ki: min: 30, max: 42 (nM) from 2 assay(s)
Kd: min: 3, max: 1.70e+4 (nM) from 31 assay(s)
IC50: min: 50, max: 420 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.937α = 90
b = 132.425β = 90
c = 56.551γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Tromso Research FoundationNorway--

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description