23ES | pdb_000023es

Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 11

PDB DOI: https://doi.org/10.2210/pdb23ES/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-02-04 Released: 2026-03-25
Deposition Author(s): Xu, Z., Chen, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.200 (Depositor), 0.201 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Discovery of Naphthyridinone Derivatives as Selective PKMYT1/WEE1 Dual Inhibitors

Xu, Z.H., Chen, S.

To be published.

Macromolecule Content

Total Structure Weight: 64.6 kDa
Atom Count: 4,906
Modeled Residue Count: 563
Deposited Residue Count: 572
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase	A, B	286	Homo sapiens	Mutation(s): 0 Gene Names: PKMYT1, MYT1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99640 (Homo sapiens) Explore Q99640 Go to UniProtKB: Q99640
PHAROS: Q99640 GTEx: ENSG00000127564
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99640
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1E5A (Subject of Investigation/LOI) Query on A1E5A Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	3-azanyl-5-chloranyl-4-(7-fluoranyl-2H-indazol-4-yl)-7-methyl-1H-1,6-naphthyridin-2-one C₁₆ H₁₁ Cl F N₅ O CUNCXCTTWGBCLJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	D [auth A] E [auth A] G [auth B] H [auth B] I [auth B] D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]