8ZTX | pdb_00008ztx

Crystal Structure of Human Myt1 Kinase domain Bounded with compound 6b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.216 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Drug Design of 2-Amino-[1,1'-biphenyl]-3-carboxamide Derivatives as Selective PKMYT1 Inhibitors for the Treatment of CCNE1 -Amplified Breast Cancer.

Wang, C.Fang, Y.Zhou, Z.Liu, Z.Feng, F.Wan, X.Li, Y.Liu, S.Ding, J.Zhang, Z.M.Xie, H.Lu, X.

(2024) J Med Chem 67: 15816-15836

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01458
  • Primary Citation of Related Structures:  
    8ZTX, 8ZU2, 8ZUD, 8ZUL

  • PubMed Abstract: 

    CCNE1 amplification occurs in breast cancer and currently lacks effective therapies. PKMYT1 as a synthetic lethal target for CCNE1 amplification holds promise for the treatment of CCNE1 -amplified breast cancer. Herein, we discover a series of 2-amino-[1,1'-biphenyl]-3-carboxamide derivatives as potent and selective PKMYT1 inhibitors using structure-based drug design. The representative compound 8ma exhibited excellent potency against PKMYT1, while sparing WEE1. It also suppressed proliferation of the CCNE1 -amplified HCC1569 breast cancer cell line and showed synergistic cytotoxicity in combination with gemcitabine. PKMYT1 X-ray cocrystallography confirmed that introduction of key binding interactions between the inhibitors and residues Asp251 and Tyr121 of PKMYT1 greatly enhanced the potency and selectivity of the compounds.


  • Organizational Affiliation

    State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, 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 kinase288Homo 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D83
Query on A1D83

Download Ideal Coordinates CCD File 
B [auth A]2-azanyl-3-(2,6-dimethyl-3-oxidanyl-phenyl)-5-pyridin-4-yl-benzamide
C20 H19 N3 O2
WMCIJTOVEOXHKF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.649α = 90
b = 58.668β = 90
c = 99.241γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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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: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-09-25
    Changes: Database references