8V5I | pdb_00008v5i

Crystal structure of MAP4K4 in complex with an inhibitor

PDB DOI: https://doi.org/10.2210/pdb8V5I/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: unidentified baculovirus
Mutation(s): No

Deposited: 2023-11-30 Released: 2025-01-22
Deposition Author(s): Greasley, S.E., Diehl, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.281 (Depositor), 0.308 (DCC)
R-Value Work:
0.249 (Depositor), 0.261 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Discovery of Highly Selective Inhibitors of Microtubule-Associated Serine/Threonine Kinase-like (MASTL).

Gallego, R.A., Scales, S., Toledo, C., Auth, M., Bernier, L., Berry, M., Brun, S., Chung, L., Davis, C., Diehl, W., Dress, K., Eisele, K., Elleraas, J., Ewanicki, J., Fobian, Y., Greasley, S., Greenwald, E.C., Johnson, T.W., Khamphavong, P., Lafontaine, J., Li, J., Linton, A., Maestre, M., Miller, N., Murtaza, A., Patman, R.L., Quinlan, C.L., Ramms, D.J., Richardson, P., Sach, N., Salomon-Ferrer, R., Silva, F., Timofeevski, S., Tran, P., Tran-Dube, M., Wang, F., Wang, W., Wythes, M., Yang, S., Zou, A., VanArsdale, T., McAlpine, I.

(2024) J Med Chem 67: 19234-19246

PubMed: 39499084 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.4c01659
Primary Citation Related Structures:
8V5H, 8V5I

PubMed Abstract:
By virtue of its role in cellular proliferation, microtubule-associated serine/threonine kinase-like (MASTL) represents a novel target and a first-in-class (FIC) opportunity to provide a new impactful therapeutic agent to oncology patients. Herein, we describe a hit-to-lead optimization effort that resulted in the delivery of two highly selective MASTL inhibitors. Key strategies leveraged to enable this work included structure-based drug design (SBDD), analysis of lipophilic efficiency (LipE) and novel synthesis. The resulting advanced lead compounds enabled a tumor growth inhibition study which was pivotal in assessing the potential value of MASTL as an oncology therapeutic target.

Organizational Affiliation

Oncology Medicinal Chemistry, Pfizer Worldwide Research and Development, 10770 Science Center Drive, La Jolla, California 92121, United States.

Macromolecule Content

Total Structure Weight: 73.88 kDa
Atom Count: 4,616
Modeled Residue Count: 568
Deposited Residue Count: 640
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase kinase 4	A, B	320	Homo sapiens	Mutation(s): 0 Gene Names: MAP4K4, HGK, KIAA0687, NIK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O95819 (Homo sapiens) Explore O95819 Go to UniProtKB: O95819
PHAROS: O95819 GTEx: ENSG00000071054
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95819
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AAA (Subject of Investigation/LOI) Query on A1AAA 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]	(3M)-N~6~-(1,4-dimethyl-1H-pyrazol-3-yl)-3-(1-methyl-1H-imidazol-5-yl)-2,7-naphthyridine-1,6-diamine C₁₇ H₁₈ N₈ XPTAASNOZLTEFS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.281 (Depositor), 0.308 (DCC)
R-Value Work: 0.249 (Depositor), 0.261 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.27	α = 90
b = 93	β = 90
c = 99.27	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data scaling
autoPROC	data reduction
BUSTER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-01-22
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.