8BZP | pdb_00008bzp

JNK3 (Mitogen-activated protein kinase 10) in Complex with Compound 23 bearing a C(sp3)F2Br moiety

PDB DOI: https://doi.org/10.2210/pdb8BZP/pdb

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

Deposited: 2022-12-15 Released: 2023-08-02
Deposition Author(s): Stahlecker, J., Vaas, S., Stehle, T., Boeckler, F.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Principles and Applications of CF 2 X Moieties as Unconventional Halogen Bond Donors in Medicinal Chemistry, Chemical Biology, and Drug Discovery.

Vaas, S., Zimmermann, M.O., Schollmeyer, D., Stahlecker, J., Engelhardt, M.U., Rheinganz, J., Drotleff, B., Olfert, M., Lammerhofer, M., Kramer, M., Stehle, T., Boeckler, F.M.

(2023) J Med Chem 66: 10202-10225

PubMed: 37487500 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.3c00634
Primary Citation Related Structures:
8BZP

PubMed Abstract:
As an orthogonal principle to the established (hetero)aryl halides, we herein highlight the usefulness of CF ₂X (X = Cl, Br, or I) moieties. Using tool compounds bearing CF ₂X moieties, we study their chemical/metabolic stability and their logP/solubility, as well as the role of XB in their small molecular crystal structures. Employing QM techniques, we analyze the observed interactions, provide insights into the conformational flexibilities and preferences in the potential interaction space. For their application in molecular design, we characterize their XB donor capacities and its interaction strength dependent on geometric parameters. Implementation of CF ₂X acetamides into our HEFLibs and biophysical evaluation (STD-NMR/ITC), followed by X-ray analysis, reveals a highly interesting binding mode for fragment 23 in JNK3, featuring an XB of CF ₂Br toward the P-loop, as well as chalcogen bonds. We suggest that underexplored chemical space combined with unconventional binding modes provides excellent opportunities for patentable chemotypes for therapeutic intervention.

Organizational Affiliation

Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany.

Macromolecule Content

Total Structure Weight: 87.23 kDa
Atom Count: 5,834
Modeled Residue Count: 676
Deposited Residue Count: 728
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A, B	364	Homo sapiens	Mutation(s): 0 Gene Names: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens) Explore P53779 Go to UniProtKB: P53779
PHAROS: P53779 GTEx: ENSG00000109339
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53779
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C15 Query on C15 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain N [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	N [auth A], W [auth B], X [auth B]	N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE C₁₇ H₃₈ N O₃ S IZWSFJTYBVKZNK-UHFFFAOYSA-O		Interactions Focus chain N [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain N [auth A] Focus chain W [auth B] Focus chain X [auth B]
SWM (Subject of Investigation/LOI) Query on SWM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain P [auth B]	C [auth A], P [auth B]	2-bromanyl-2,2-bis(fluoranyl)-~{N}-(5-pyridin-4-yl-1,3,4-thiadiazol-2-yl)ethanamide C₉ H₅ Br F₂ N₄ O S QJBZKGIEISLBPK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain P [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth A]	H [auth A], L [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth A] Interactions & Density Focus chain H [auth A] Focus chain L [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	F [auth A] I [auth A] M [auth A] O [auth B] S [auth B] F [auth A], I [auth A], M [auth A], O [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain E [auth A]	D [auth A] E [auth A] J [auth A] K [auth A] Q [auth B] D [auth A], E [auth A], J [auth A], K [auth A], Q [auth B], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]