8P9B

Crystal Structure of Mnk2-D228G in complex with Tinodasertib

• PDB DOI: https://doi.org/10.2210/pdb8P9B/pdb

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


• Deposited: 2023-06-05 Released: 2024-06-12 
• Deposition Author(s): Turnbull, A.P., Sabin, V., Bell, C., Watson, M.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.264 
• R-Value Work: 0.208 

Starting Model: experimental

Literature

Crystal Structure of Mnk2-D228G in complex with Tinodasertib

Sabin, V., Turnbull, A.P., Bell, C., Watson, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.08 kDa 
• Atom Count: 2,047 
• Modelled Residue Count: 263 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP kinase-interacting serine/threonine-protein kinase 2	A	316	Homo sapiens	Mutation(s): 1  Gene Names: MKNK2, GPRK7, MNK2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBH9 (Homo sapiens) Explore Q9HBH9  Go to UniProtKB:  Q9HBH9
PHAROS:  Q9HBH9 GTEx:  ENSG00000099875

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X8K (Subject of Investigation/LOI)	C [auth A]	4-[6-(4-morpholin-4-ylcarbonylphenyl)imidazo[1,2-a]pyridin-3-yl]benzenecarbonitrile C25 H20 N4 O2 FWRFPHJSGLYXTD-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
X8K	BindingDB:  8P9B	IC50: min: 9.4, max: 321 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.264 
• R-Value Work: 0.208 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.91	α = 90
b = 105.91	β = 90
c = 71.5	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Turnbull, A.P., Sabin, V., Bell, C., Watson, M.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	--

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release