6CKX

Structure of CDK12/CycK in complex with a small molecule inhibitor N-(4-(1-methyl-1H-pyrazol-4-yl)phenyl)-N-((1r,4r)-4-(quinazolin-2-ylamino)cyclohexyl)acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of 3-Benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea Derivatives as Novel and Selective Cyclin-Dependent Kinase 12 (CDK12) Inhibitors.

Ito, M.Tanaka, T.Toita, A.Uchiyama, N.Kokubo, H.Morishita, N.Klein, M.G.Zou, H.Murakami, M.Kondo, M.Sameshima, T.Araki, S.Endo, S.Kawamoto, T.Morin, G.B.Aparicio, S.A.Nakanishi, A.Maezaki, H.Imaeda, Y.

(2018) J. Med. Chem. 61: 7710-7728

  • DOI: 10.1021/acs.jmedchem.8b00683

  • PubMed Abstract: 
  • Cyclin-dependent kinase 12 (CDK12) plays a key role in the coordination of transcription with elongation and mRNA processing. CDK12 mutations found in tumors and CDK12 inhibition sensitize cancer cells to DNA-damaging reagents and DNA-repair inhibito ...

    Cyclin-dependent kinase 12 (CDK12) plays a key role in the coordination of transcription with elongation and mRNA processing. CDK12 mutations found in tumors and CDK12 inhibition sensitize cancer cells to DNA-damaging reagents and DNA-repair inhibitors. This suggests that CDK12 inhibitors are potential therapeutics for cancer that may cause synthetic lethality. Here, we report the discovery of 3-benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea derivatives as novel and selective CDK12 inhibitors. Structure-activity relationship studies of a HTS hit, structure-based drug design, and conformation-oriented design using the Cambridge Structural Database afforded the optimized compound 2, which exhibited not only potent CDK12 (and CDK13) inhibitory activity and excellent selectivity but also good physicochemical properties. Furthermore, 2 inhibited the phosphorylation of Ser2 in the C-terminal domain of RNA polymerase II and induced growth inhibition in SK-BR-3 cells. Therefore, 2 represents an excellent chemical probe for functional studies of CDK12 and could be a promising lead compound for drug discovery.


    Organizational Affiliation

    Genome Sciences Centre , British Columbia Cancer Agency , 675 West 10th Avenue , Vancouver , British Columbia V5Z 1L3 , Canada.,Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan.,Department of Medical Genetics , University of British Columbia , Vancouver , British Columbia V6H 3N1 , Canada.,Department of Molecular Oncology , British Columbia Cancer Agency , 675 West 10th Avenue , Vancouver , British Columbia V5Z 1L3 , Canada.,Department of Structural Biology , Takeda California Inc. , 10410 Science Center Drive , San Diego , California 92121 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 12
A, C
351Homo sapiensMutation(s): 0 
Gene Names: CDK12 (CRK7, CRKRS, KIAA0904)
EC: 2.7.11.22, 2.7.11.23
Find proteins for Q9NYV4 (Homo sapiens)
Go to Gene View: CDK12
Go to UniProtKB:  Q9NYV4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-K
B, D
268Homo sapiensMutation(s): 0 
Gene Names: CCNK (CPR4)
Find proteins for O75909 (Homo sapiens)
Go to Gene View: CCNK
Go to UniProtKB:  O75909
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8M1
Query on 8M1

Download SDF File 
Download CCD File 
A, C
N-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]-N-{trans-4-[(quinazolin-2-yl)amino]cyclohexyl}acetamide
C26 H28 N6 O
FNRJTMUROZAOIB-HCGLCNNCSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.596α = 90.00
b = 107.530β = 90.00
c = 138.324γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-03-01 
  • Released Date: 2018-08-29 
  • Deposition Author(s): Klein, M.G.

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-26
    Type: Data collection, Database references