5MTY

Dibenzosuberone inhibitor 8e in complex with p38 MAPK

• PDB DOI: https://doi.org/10.2210/pdb5MTY/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-11 Released: 2017-09-06 
• Deposition Author(s): Buehrmann, M., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.271 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

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: 42.48 kDa 
• Atom Count: 2,733 
• Modelled Residue Count: 328 
• 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): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A 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
HB9	B [auth A]	~{N}-[2,4-bis(fluoranyl)-5-[[14-(2-hydroxyethylcarbamoyl)-2-oxidanylidene-6-tricyclo[9.4.0.0^{3,8}]pentadeca-1(15),3(8),4,6,11,13-hexaenyl]amino]phenyl]thiophene-2-carboxamide C29 H23 F2 N3 O4 S ZBPQDEQSQUZYHD-UHFFFAOYSA-N
BOG	C [auth A], D [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HB9	BindingDB:  5MTY	Kd: min: 1.3, max: 7.5 (nM) from 2 assay(s)
		IC50: min: 0.6, max: 35 (nM) from 2 assay(s)
	Binding MOAD:  5MTY	Kd: 1.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.271 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.118	α = 90
b = 70.179	β = 90
c = 74.86	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Buehrmann, M., Rauh, D.

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Database references
• Version 1.2: 2017-10-25
  Changes: Database references
• Version 1.3: 2019-08-14
  Changes: Data collection
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary