8H6T

Complex structure of CDK2/Cyclin E1 and a potent, selective small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.254 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Accelerated Discovery of Macrocyclic CDK2 Inhibitor QR-6401 by Generative Models and Structure-Based Drug Design.

Yu, Y.Huang, J.He, H.Han, J.Ye, G.Xu, T.Sun, X.Chen, X.Ren, X.Li, C.Li, H.Huang, W.Liu, Y.Wang, X.Gao, Y.Cheng, N.Guo, N.Chen, X.Feng, J.Hua, Y.Liu, C.Zhu, G.Xie, Z.Yao, L.Zhong, W.Chen, X.Liu, W.Li, H.

(2023) ACS Med Chem Lett 14: 297-304

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00515
  • Primary Citation of Related Structures:  
    8H6P, 8H6T

  • PubMed Abstract: 

    Selective CDK2 inhibitors have the potential to provide effective therapeutics for CDK2-dependent cancers and for combating drug resistance due to high cyclin E1 (CCNE1) expression intrinsically or CCNE1 amplification induced by treatment of CDK4/6 inhibitors. Generative models that take advantage of deep learning are being increasingly integrated into early drug discovery for hit identification and lead optimization. Here we report the discovery of a highly potent and selective macrocyclic CDK2 inhibitor QR-6401 ( 23 ) accelerated by the application of generative models and structure-based drug design (SBDD). QR-6401 ( 23 ) demonstrated robust antitumor efficacy in an OVCAR3 ovarian cancer xenograft model via oral administration.


  • Organizational Affiliation

    Tencent AI Lab, Tencent, Shenzhen 518057, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
G1/S-specific cyclin-E1272Homo sapiensMutation(s): 0 
Gene Names: CCNE1CCNE
UniProt & NIH Common Fund Data Resources
Find proteins for P24864 (Homo sapiens)
Explore P24864 
Go to UniProtKB:  P24864
PHAROS:  P24864
GTEx:  ENSG00000105173 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24864
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WZZ (Subject of Investigation/LOI)
Query on WZZ

Download Ideal Coordinates CCD File 
C [auth A](1R,3S)-3-{3-[(pyridin-2-yl)amino]-1H-pyrazol-5-yl}cyclopentyl propan-2-ylcarbamate
C17 H23 N5 O2
RNCRMJAZEFHCPK-QWHCGFSZSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.254 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.97α = 90
b = 101.97β = 90
c = 151.617γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2023-02-22 
  • Deposition Author(s): Ren, X.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary