4YC8 | pdb_00004yc8

C-Helix-Out Binding of Dasatinib Analog to c-Abl Kinase

PDB DOI: https://doi.org/10.2210/pdb4YC8/pdb

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

Deposited: 2015-02-19 Released: 2016-03-02
Deposition Author(s): Kwarcinski, F.E., Brandvold, K.B., Johnson, T.J., Phadke, S., Meagher, J.L., Seeliger, M.A., Stuckey, J.A., Soellner, M.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity.

Kwarcinski, F.E., Brandvold, K.R., Phadke, S., Beleh, O.M., Johnson, T.K., Meagher, J.L., Seeliger, M.A., Stuckey, J.A., Soellner, M.B.

(2016) ACS Chem Biol 11: 1296-1304

PubMed: 26895387 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acschembio.5b01018
Primary Citation Related Structures:
4YBJ, 4YBK, 4YC8

PubMed Abstract:
In the kinase field, there are many widely held tenets about conformation-selective inhibitors that have yet to be validated using controlled experiments. We have designed, synthesized, and characterized a series of kinase inhibitor analogues of dasatinib, an FDA-approved kinase inhibitor that binds the active conformation. This inhibitor series includes two Type II inhibitors that bind the DFG-out inactive conformation and two inhibitors that bind the αC-helix-out inactive conformation. Using this series of compounds, we analyze the impact that conformation-selective inhibitors have on target binding and kinome-wide selectivity.

Organizational Affiliation

Department of Pharmacological Sciences, Stony Brook University , Stony Brook, New York 11794, United States.

Macromolecule Content

Total Structure Weight: 68.02 kDa
Atom Count: 4,189
Modeled Residue Count: 523
Deposited Residue Count: 574
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ABL1	A, B	287	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00519
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4B7 Query on 4B7 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-N-(4-phenoxyphenyl)-1,3-thiazole-5-carboxamide C₂₇ H₂₉ N₇ O₃ S QUFCHHSHOLSVOT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
4B7	BindingDB: 4YC8	Kd: 14 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.76	α = 90
b = 127.1	β = 90
c = 57.17	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-03-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-02
Type: Initial release
Version 1.1: 2016-06-01
Changes: Database references
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description