2PUU | pdb_00002puu

Crystal structure of p38 complex with 1-(5-tert-Butyl-2-p-tolyl-2H-pyrazol-3-yl)-3-[4-(6-morpholin-4-ylmethyl-pyridin-3-yl)naphthalen-1-yl]urea

PDB DOI: https://doi.org/10.2210/pdb2PUU/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-05-09 Released: 2008-05-20
Deposition Author(s): Qian, K.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.318 (Depositor), 0.310 (DCC)
R-Value Work:
0.228 (Depositor), 0.220 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

A new class of p38 MAP kinase inhibitors based on the pyrazole-naphthyl urea scaffold

Qian, K.C.

To be published.

Macromolecule Content

Total Structure Weight: 40.38 kDa
Atom Count: 2,744
Modelled Residue Count: 330
Deposited Residue Count: 348
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	348	Mus musculus	Mutation(s): 1 Gene Names: Mapk14, Crk1, Csbp1, Csbp2 EC: 2.7.11.24
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 LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G2G Query on G2G 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]	5-TERT-BUTYL-2-(4-METHYLPHENYL)-3-{[({4-[6-(MORPHOLIN-4-YLMETHYL)PYRIDIN-3-YL]-1-NAPHTHYL}AMINO)CARBONYL]AMINO}-1H-PYRAZOL-2-IUM C₃₅ H₃₉ N₆ O₂ AJSMPUSEUKXNDW-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.318 (Depositor), 0.310 (DCC)
R-Value Work: 0.228 (Depositor), 0.220 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.908	α = 90
b = 74.722	β = 90
c = 78.245	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-05-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-05-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-04-04
Changes: Data collection
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2024-02-21
Changes: Data collection

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.