6YQ1 | pdb_00006yq1

FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH N-Methyl-N-(3-{[2-(2-oxo-1,2,3,4-tetrahydro-quinolin-6-ylamino)-5-trifluoromethyl-pyrimidin-4-ylamino]-methyl}-pyridin-2-yl)-methanesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb6YQ1/pdb

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


• Deposited: 2020-04-16 Released: 2021-02-10 
• Deposition Author(s): Musil, D., Heinrich, T., Amaral, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.214 (Depositor) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2.

Berger, B.T., Amaral, M., Kokh, D.B., Nunes-Alves, A., Musil, D., Heinrich, T., Schroder, M., Neil, R., Wang, J., Navratilova, I., Bomke, J., Elkins, J.M., Muller, S., Frech, M., Wade, R.C., Knapp, S.

(2021) Cell Chem Biol 28: 686

• PubMed: 33497606 
• DOI: https://doi.org/10.1016/j.chembiol.2021.01.003
• Primary Citation Related Structures: 
  6YOJ, 6YQ1, 6YR9, 6YT6, 6YVS, 6YVY, 6YXV


• PubMed Abstract: 
  

  There is increasing evidence of a significant correlation between prolonged drug-target residence time and increased drug efficacy. Here, we report a structural rationale for kinetic selectivity between two closely related kinases: focal adhesion kinase (FAK) and proline-rich tyrosine kinase 2 (PYK2). We found that slowly dissociating FAK inhibitors induce helical structure at the DFG motif of FAK but not PYK2. Binding kinetic data, high-resolution structures and mutagenesis data support the role of hydrophobic interactions of inhibitors with the DFG-helical region, providing a structural rationale for slow dissociation rates from FAK and kinetic selectivity over PYK2. Our experimental data correlate well with computed relative residence times from molecular simulations, supporting a feasible strategy for rationally optimizing ligand residence times. We suggest that the interplay between the protein structural mobility and ligand-induced effects is a key regulator of the kinetic selectivity of inhibitors of FAK versus PYK2.

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Organizational Affiliation: 
• Structural Genomics Consortium, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany; Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany.
Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany; Instituto de Biologia Experimental e Tecnológica, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal.
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany.
Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.
Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany.
Structural Genomics Consortium, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany; Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany; German Cancer network DKTK and Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt am Main, Germany. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 131.42 kDa 
• Atom Count: 9,732 
• Modeled Residue Count: 1,065 
• Deposited Residue Count: 1,128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Focal adhesion kinase 1	A, B, C, D	282	Homo sapiens	Mutation(s): 0  Gene Names: PTK2, FAK, FAK1 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q05397 (Homo sapiens) Explore Q05397  Go to UniProtKB:  Q05397
PHAROS:  Q05397 GTEx:  ENSG00000169398

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P7N (Subject of Investigation/LOI)	E [auth A], H [auth B], I [auth C], J [auth D]	~{N}-methyl-~{N}-[3-[[[2-[(2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl]amino]methyl]pyridin-2-yl]methanesulfonamide C22 H22 F3 N7 O3 S MUVVMGFRHXQCRG-UHFFFAOYSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P7N	BindingDB:  6YQ1	Ki: 3.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.214 (Depositor) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.532	α = 90
b = 75.749	β = 102.37
c = 173.265	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Musil, D., Heinrich, T., Amaral, M.

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2021-06-02
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary