3LFE | pdb_00003lfe

Human p38 MAP Kinase in Complex with RL116

• PDB DOI: https://doi.org/10.2210/pdb3LFE/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-01-16 Released: 2011-04-20 
• Deposition Author(s): Gruetter, C., Simard, J.R., Getlik, M., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.274 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Development of novel thiazole-urea compounds which stabalize the inactive conformation of p38 alpha

Getlik, M., Gruetter, C., Simard, J.R., Van Otterlo, W., Robubi, A., Aust, B., Rauh, D.

To be published.

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: 42.02 kDa 
• Atom Count: 2,817 
• Modeled Residue Count: 334 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 4  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539 GTEx:  ENSG00000112062

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z84	C [auth A]	1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-{4-[2-(pyridin-4-ylmethoxy)ethyl]-1,3-thiazol-2-yl}urea C26 H30 N6 O2 S DZVQBRGQNWDWIG-UHFFFAOYSA-N
BOG	B [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Z84	BindingDB:  3LFE	Kd: 586 (nM) from 1 assay(s)
		IC50: 586 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.274 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.63	α = 90
b = 70.16	β = 90
c = 74.18	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Gruetter, C., Simard, J.R., Getlik, M., Rauh, D.

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2021-10-13
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description