7RA5 | pdb_00007ra5

CDK2 IN COMPLEX WITH COMPOUND 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 
    0.274 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.225 (Depositor) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of SY-5609: A Selective, Noncovalent Inhibitor of CDK7.

Marineau, J.J.Hamman, K.B.Hu, S.Alnemy, S.Mihalich, J.Kabro, A.Whitmore, K.M.Winter, D.K.Roy, S.Ciblat, S.Ke, N.Savinainen, A.Wilsily, A.Malojcic, G.Zahler, R.Schmidt, D.Bradley, M.J.Waters, N.J.Chuaqui, C.

(2022) J Med Chem 65: 1458-1480

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01171
  • Primary Citation Related Structures: 
    7RA5

  • PubMed Abstract: 

    CDK7 has emerged as an exciting target in oncology due to its roles in two important processes that are misregulated in cancer cells: cell cycle and transcription. This report describes the discovery of SY-5609 , a highly potent (sub-nM CDK7 K d ) and selective, orally available inhibitor of CDK7 that entered the clinic in 2020 (ClinicalTrials.gov Identifier: NCT04247126). Structure-based design was leveraged to obtain high selectivity (>4000-times the closest off target) and slow off-rate binding kinetics desirable for potent cellular activity. Finally, incorporation of a phosphine oxide as an atypical hydrogen bond acceptor helped provide the required potency and metabolic stability. The development candidate SY-5609 displays potent inhibition of CDK7 in cells and demonstrates strong efficacy in mouse xenograft models when dosed as low as 2 mg/kg.


  • Organizational Affiliation
    • Syros Pharmaceuticals Inc., 35 Cambridge Park Drive, Fourth Floor, Cambridge, Massachusetts 02140, United States.

Macromolecule Content 

  • Total Structure Weight: 34.54 kDa 
  • Atom Count: 2,458 
  • Modeled Residue Count: 278 
  • Deposited Residue Count: 300 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2300Homo 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

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3I3
(Subject of Investigation/LOI)

Query on 3I3



Download:Ideal Coordinates CCD File
B [auth A]4-[7-(methanesulfonyl)-1H-indol-3-yl]-N-[(3S)-piperidin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine
C19 H20 F3 N5 O2 S
NUMHIIKAGFNIFT-NSHDSACASA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free:  0.274 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.225 (Depositor) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.615α = 90
b = 72.272β = 90
c = 70.818γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2022-05-18
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description