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)

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42684
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STI Query on STI Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-04-21

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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