7NXJ

Crystal structure of human Cdk13/Cyclin K in complex with the inhibitor THZ531


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Structure-activity relationship study of THZ531 derivatives enables the discovery of BSJ-01-175 as a dual CDK12/13 covalent inhibitor with efficacy in Ewing sarcoma.

Jiang, B.Jiang, J.Kaltheuner, I.H.Iniguez, A.B.Anand, K.Ferguson, F.M.Ficarro, S.B.Seong, B.K.A.Greifenberg, A.K.Dust, S.Kwiatkowski, N.P.Marto, J.A.Stegmaier, K.Zhang, T.Geyer, M.Gray, N.S.

(2021) Eur J Med Chem 221: 113481-113481

  • DOI: https://doi.org/10.1016/j.ejmech.2021.113481
  • Primary Citation of Related Structures:  
    7NXJ, 7NXK

  • PubMed Abstract: 

    Development of inhibitors targeting CDK12/13 is of increasing interest as a potential therapy for cancers as these compounds inhibit transcription of DNA damage response (DDR) genes. We previously described THZ531, a covalent inhibitor with selectivity for CDK12/13. In order to elucidate structure-activity relationship (SAR), we have undertaken a medicinal chemistry campaign and established a focused library of THZ531 analogs. Among these analogs, BSJ-01-175 demonstrates exquisite selectivity, potent inhibition of RNA polymerase II phosphorylation, and downregulation of CDK12-targeted genes in cancer cells. A 3.0 Å co-crystal structure with CDK12/CycK provides a structural rational for selective targeting of Cys1039 located in a C-terminal extension from the kinase domain. With moderate pharmacokinetic properties, BSJ-01-175 exhibits efficacy against an Ewing sarcoma tumor growth in a patient-derived xenograft (PDX) mouse model following 10 mg/kg once a day, intraperitoneal administration. Taken together, BSJ-01-175 represents the first selective CDK12/13 covalent inhibitor with in vivo efficacy reported to date.


  • Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 13
A, C
347Homo sapiensMutation(s): 0 
Gene Names: CDK13CDC2LCDC2L5CHEDKIAA1791
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14004 (Homo sapiens)
Explore Q14004 
Go to UniProtKB:  Q14004
PHAROS:  Q14004
GTEx:  ENSG00000065883 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14004
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-K
B, D
268Homo sapiensMutation(s): 0 
Gene Names: CCNKCPR4
UniProt & NIH Common Fund Data Resources
Find proteins for O75909 (Homo sapiens)
Explore O75909 
Go to UniProtKB:  O75909
PHAROS:  O75909
GTEx:  ENSG00000090061 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75909
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5I1 (Subject of Investigation/LOI)
Query on 5I1

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
N-[4-[(3R)-3-[[5-chloranyl-4-(1H-indol-3-yl)pyrimidin-2-yl]amino]piperidin-1-yl]carbonylphenyl]-4-(dimethylamino)butanamide
C30 H34 Cl N7 O2
ZVKCKFIOVYZRHX-JOCHJYFZSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.88α = 90
b = 149.45β = 94.61
c = 92.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 5I1Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyGE 976/9-2
German Research Foundation (DFG)GermanyEXC2151-390873048

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary