3P5K

P38 inhibitor-bound

• PDB DOI: https://doi.org/10.2210/pdb3P5K/pdb

• Classification: TRANSFERASE/transferase inhibitor
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-08 Released: 2011-11-02 
• Deposition Author(s): Namboodiri, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.265 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.88 kDa 
• Atom Count: 2,841 
• Modelled Residue Count: 332 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	366	Mus musculus	Mutation(s): 0  Gene Names: Mapk14, Crk1, Csbp1, Csbp2 EC: 2.7.11.24
UniProt
Find proteins for P47811 (Mus musculus) Explore P47811  Go to UniProtKB:  P47811

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P5K	C [auth A]	1-{5-tert-butyl-3-[(1,1-dioxidothiomorpholin-4-yl)carbonyl]thiophen-2-yl}-3-naphthalen-1-ylurea C24 H27 N3 O4 S2 MGCVZCZJPOZRQX-UHFFFAOYSA-N
BOG	B [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P5K	Binding MOAD:  3P5K	IC50: 76 (nM) from 1 assay(s)
	PDBBind:  3P5K	IC50: 76 (nM) from 1 assay(s)
	BindingDB:  3P5K	IC50: 76 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.265 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.95	α = 90
b = 71.08	β = 90
c = 75.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Namboodiri, H.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2011-11-09
  Changes: Database references
• Version 1.2: 2012-01-25
  Changes: Database references
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references, Structure summary