3GVU

The crystal structure of human ABL2 in complex with GLEEVEC

• PDB DOI: https://doi.org/10.2210/pdb3GVU/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2009-03-31 Released: 2009-04-21 
• Deposition Author(s): Ugochukwu, E., Salah, E., Barr, A., Mahajan, P., Shrestha, B., Savitsky, P., Chaikuad, A., Filippakopoulos, P., Roos, A., Pike, A.C.W., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.226 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

The crystal structure of human ABL2 in complex with GLEEVEC

Salah, E., Ugochukwu, E., Barr, A., Mahajan, P., Shrestha, B., Savitsky, P., Knapp, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.53 kDa 
• Atom Count: 2,432 
• Modelled Residue Count: 271 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ABL2	A	292	Homo sapiens	Mutation(s): 0  Gene Names: ABL2 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P42684 (Homo sapiens) Explore P42684  Go to UniProtKB:  P42684
PHAROS:  P42684 GTEx:  ENSG00000143322

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STI	B [auth A], C [auth A]	4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE C29 H31 N7 O KTUFNOKKBVMGRW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
STI	BindingDB:  3GVU	Ki: min: 13, max: 7000 (nM) from 5 assay(s)
		Kd: min: 1, max: 1.00e+4 (nM) from 34 assay(s)
		IC50: min: 1.1, max: 1.00e+4 (nM) from 66 assay(s)
		EC50: min: 34, max: 1000 (nM) from 4 assay(s)
	PDBBind:  3GVU	Kd: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.226 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.46	α = 90
b = 99.44	β = 90
c = 87.81	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Ugochukwu, E., Salah, E., Barr, A., Mahajan, P., Shrestha, B., Savitsky, P., Chaikuad, A., Filippakopoulos, P., Roos, A., Pike, A.C.W., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary