Experimental Data Snapshot

  • Resolution: 1.67 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.230 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


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 of Related Structures:  

  • 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2300Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
  • 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
Experimental Data & Validation

Experimental Data

  • Resolution: 1.67 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.230 
  • 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
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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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