4KKH | pdb_00004kkh

The crystal structure of inhibitor-bound JNK3

PDB DOI: https://doi.org/10.2210/pdb4KKH/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-06 Released: 2014-05-21
Deposition Author(s): Han, B.G., Shim, M.B., Ahn, H.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.277 (Depositor), 0.280 (DCC)
R-Value Work:
0.229 (Depositor), 0.230 (DCC)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The crystal structure of AMP, apo, and inhibitor-bound JNK3

Han, B.G., Shim, M.B., Ahn, H.C.

To be published.

Macromolecule Content

Total Structure Weight: 42.62 kDa
Atom Count: 3,042
Modeled Residue Count: 351
Deposited Residue Count: 365
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	365	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53779
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1RQ Query on 1RQ 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]	cyclopropyl[(3R)-3-({4-[6-hydroxy-2-(naphthalen-2-yl)-1H-benzimidazol-1-yl]pyrimidin-2-yl}amino)piperidin-1-yl]methanone C₃₀ H₂₈ N₆ O₂ GQWKCVUFYCHSLR-HSZRJFAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
1RQ	BindingDB: 4KKH	Kd: 46 (nM) from 1 assay(s)
1RQ	BindingDB: 4KKH	IC50: 1090 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.277 (Depositor), 0.280 (DCC)
R-Value Work: 0.229 (Depositor), 0.230 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.324	α = 90
b = 71.499	β = 90
c = 107.081	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-05-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-21
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.