4ZOG

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

• PDB DOI: https://doi.org/10.2210/pdb4ZOG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-06 Released: 2016-09-14 
• Deposition Author(s): Kyomuhendo, P., Narayanan, D., Engh, R.A.
• Funding Organization(s): Tromso Research Foundation

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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

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.89 kDa 
• Atom Count: 4,479 
• Modelled Residue Count: 537 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ABL1	A, B	283	Homo sapiens	Mutation(s): 0  Gene Names: ABL1, ABL, JTK7 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VX6	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	H [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
MXE	D [auth A], E [auth A], F [auth A]	2-METHOXYETHANOL C3 H8 O2 XNWFRZJHXBZDAG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 105.937	α = 90
b = 132.425	β = 90
c = 56.551	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Kyomuhendo, P., Narayanan, D., Engh, R.A.

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Funding Organization	Location	Grant Number
Tromso Research Foundation	Norway	--

Revision History  

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