9LGN | pdb_00009lgn

Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.241 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

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 and Potent PKMYT1 Inhibitors with Antitumor Efficacy.

Chen, B.Liu, X.Mu, T.Xu, J.Zhao, D.Dey, F.Tang, Y.Xu, Z.Yang, J.Huang, K.Li, C.Chen, S.Zhu, S.Wang, S.Yao, X.Yan, Z.Tu, Y.Dai, Y.Qiu, H.Yang, J.Jiang, T.Qi, Y.Li, Y.Shen, H.C.Zhu, W.Tan, X.Wu, J.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00114
  • Primary Citation of Related Structures:  
    9LGN, 9LGV

  • PubMed Abstract: 

    PKMYT1 is a crucial regulator of the cell cycle, particularly involved in the G2/M transition through the inhibitory phosphorylation of CDK1, and is a promising therapeutic target for cancer therapy. Data mining in the Roche kinome screen database identified a hit characterized by 100% PKMYT1 inhibitory activity at a 10 μM concentration, which was further validated with a PKMYT1 enzymatic assay showing double-digit nanomolar potency. The hit featured a quinolinone central core and a phenol headgroup. The replacement of the problematic phenol headgroup with an indazole moiety induced a flip in the kinase hinge cysteine and glycine residues, resulting in a series of derivatives with enhanced potency, superior kinome selectivity, and no GSH flag. Further structural fine-tuning led to the discovery of compound 36 , a novel, selective, and potent PKMYT1 inhibitor with favorable oral pharmacokinetic profiles and promising in vivo antitumor efficacy.


  • Organizational Affiliation

    Medicinal Chemistry, China Innovation Center of Roche, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
A, B
286Homo sapiensMutation(s): 0 
Gene Names: PKMYT1MYT1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99640
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EJU (Subject of Investigation/LOI)
Query on A1EJU

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
3-azanyl-4-(7-fluoranyl-2H-indazol-4-yl)-8-methoxy-1H-1,5-naphthyridin-2-one
C16 H12 F N5 O2
CMDVDQKZWRQICJ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.45α = 90
b = 110.405β = 109.97
c = 72.019γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
autoPROCdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release