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), 0.316 (DCC)
R-Value Work:
0.228 (Depositor), 0.227 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 2PUU

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
Modeled Residue Count: 330
Deposited Residue Count: 348
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P47811
Sequence Annotations Expand
Reference Sequence

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), 0.316 (DCC)
R-Value Work: 0.228 (Depositor), 0.227 (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

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.