3IW5

Human p38 MAP Kinase in Complex with an Indole Derivative

• PDB DOI: https://doi.org/10.2210/pdb3IW5/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-09-02 Released: 2009-11-17 
• Deposition Author(s): Gruetter, C., Simard, J.R., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.291 
• R-Value Work: 0.205 
• R-Value Observed: 0.211 

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: 42.38 kDa 
• Atom Count: 2,851 
• Modelled Residue Count: 336 
• 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
DF3	C [auth A]	N-[2-(3-{[2-(2,3-dihydro-1,4-benzodioxin-6-ylamino)-2-oxoethyl]sulfanyl}-1H-indol-1-yl)ethyl]-3-(trifluoromethyl)benzamide C28 H24 F3 N3 O4 S BNPQVUSGXCJYEF-UHFFFAOYSA-N
BOG	B [auth A], D [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DF3	PDBBind:  3IW5	Kd: 839 (nM) from 1 assay(s)
	Binding MOAD:  3IW5	Kd: 839 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.291 
• R-Value Work: 0.205 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.07	α = 90
b = 70.05	β = 90
c = 74.05	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Gruetter, C., Simard, J.R., Rauh, D.

Revision History  

• Version 1.0: 2009-11-17
  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: 2021-11-10
  Changes: Database references, Structure summary
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description