2EWA

Dual binding mode of pyridinylimidazole to MAP kinase p38

PDB DOI: https://doi.org/10.2210/pdb2EWA/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-11-02 Released: 2006-08-01
Deposition Author(s): Delarbre, L., Pouzieux, S., Guilloteau, J.-P., Michot, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.279
R-Value Work: 0.241

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

NMR characterization of kinase p38 dynamics in free and ligand-bound forms.

Vogtherr, M., Saxena, K., Hoelder, S., Grimme, S., Betz, M., Schieborr, U., Pescatore, B., Robin, M., Delarbre, L., Langer, T., Wendt, K.U., Schwalbe, H.

(2006) Angew Chem Int Ed Engl 45: 993-997

PubMed: 16374788 Search on PubMed
DOI: https://doi.org/10.1002/anie.200502770
Primary Citation of Related Structures:
2EWA

Organizational Affiliation

Johann Wolfgang Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Germany.

Macromolecule Content

Total Structure Weight: 43.76 kDa
Atom Count: 2,815
Modelled Residue Count: 330
Deposited Residue Count: 379
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 14	A	379	Mus musculus	Mutation(s): 0 Gene Names: Mapk14, Crk1, Csbp1, Csbp2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
UniProt
Find proteins for P47811 (Mus musculus) Explore P47811 Go to UniProtKB: P47811
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P47811
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SB2 Query on SB2 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]	4-[5-(4-FLUORO-PHENYL)-2-(4-METHANESULFINYL-PHENYL)-3H-IMIDAZOL-4-YL]-PYRIDINE C₂₁ H₁₆ F N₃ O S CDMGBJANTYXAIV-MHZLTWQESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
SB2	PDBBind: 2EWA	Kd: 11.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.279
R-Value Work: 0.241
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.192	α = 90
b = 74.65	β = 90
c = 78.261	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-08-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-01
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations