4L7F | pdb_00004l7f

Co-crystal Structure of JNK1 and AX13587

PDB DOI: https://doi.org/10.2210/pdb4L7F/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2013-06-13 Released: 2013-08-21
Deposition Author(s): Walter, R.L., Ranieri, G.M., Riggs, A.M., Weissig, H., Li, B., Shreder, K.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.198 (Depositor), 0.196 (DCC)
R-Value Work:
0.161 (Depositor), 0.161 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Hit-to-lead optimization and kinase selectivity of imidazo[1,2-a]quinoxalin-4-amine derived JNK1 inhibitors.

Li, B., Cociorva, O.M., Nomanbhoy, T., Weissig, H., Li, Q., Nakamura, K., Liyanage, M., Zhang, M.C., Shih, A.Y., Aban, A., Hu, Y., Cajica, J., Pham, L., Kozarich, J.W., Shreder, K.R.

(2013) Bioorg Med Chem Lett 23: 5217-5222

PubMed: 23916259 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2013.06.087
Primary Citation Related Structures:
4L7F

PubMed Abstract:
As the result of a rhJNK1 HTS, the imidazo[1,2-a]quinoxaline 1 was identified as a 1.6 μM rhJNK1 inhibitor. Optimization of this compound lead to AX13587 (rhJNK1 IC50=160 nM) which was co-crystallized with JNK1 to identify key molecular interactions. Kinase profiling against 125+ kinases revealed AX13587 was an inhibitor of JNK, MAST3, and MAST4 whereas its methylene homolog AX14373 (native JNK1 IC50=47 nM) was a highly specific JNK inhibitor.

Organizational Affiliation

ActivX Biosciences, Inc., 11025 N. Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 42.84 kDa
Atom Count: 3,554
Modeled Residue Count: 354
Deposited Residue Count: 367
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 8	A	367	Homo sapiens	Mutation(s): 0 Gene Names: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45983 (Homo sapiens) Explore P45983 Go to UniProtKB: P45983
PHAROS: P45983 GTEx: ENSG00000107643
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45983
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1V5 Query on 1V5 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-[1-(4-fluorophenyl)cyclopropyl]-4-[(trans-4-hydroxycyclohexyl)amino]imidazo[1,2-a]quinoxaline-8-carboxamide C₂₆ H₂₆ F N₅ O₂ MFJOWCFANZXQBU-MXVIHJGJSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.198 (Depositor), 0.196 (DCC)
R-Value Work: 0.161 (Depositor), 0.161 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.802	α = 90
b = 135.802	β = 90
c = 94.208	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-08-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-21
Type: Initial release
Version 1.1: 2013-10-09
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations