8P9B | pdb_00008p9b

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.264 (Depositor), 0.260 (DCC)
R-Value Work:
0.208 (Depositor), 0.213 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure of Mnk2-D228G in complex with Tinodasertib

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

To be published.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HBH9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
X8K (Subject of Investigation/LOI) Query on X8K Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-[6-(4-morpholin-4-ylcarbonylphenyl)imidazo[1,2-a]pyridin-3-yl]benzenecarbonitrile C₂₅ H₂₀ N₄ O₂ FWRFPHJSGLYXTD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.264 (Depositor), 0.260 (DCC)
R-Value Work: 0.208 (Depositor), 0.213 (DCC)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-12

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.