6B3E

Crystal structure of human CDK12/CyclinK in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-Based Design of Selective Noncovalent CDK12 Inhibitors.

Johannes, J.W.Denz, C.R.Su, N.Wu, A.Impastato, A.C.Mlynarski, S.Varnes, J.G.Prince, D.B.Cidado, J.Gao, N.Haddrick, M.Jones, N.H.Li, S.Li, X.Liu, Y.Nguyen, T.B.O'Connell, N.Rivers, E.Robbins, D.W.Tomlinson, R.Yao, T.Zhu, X.Ferguson, A.D.Lamb, M.L.Manchester, J.I.Guichard, S.

(2018) ChemMedChem 13: 231-235

  • DOI: 10.1002/cmdc.201700695

  • PubMed Abstract: 
  • Cyclin-dependent kinase (CDK) 12 knockdown via siRNA decreases the transcription of DNA-damage-response genes and sensitizes BRCA wild-type cells to poly(ADP-ribose) polymerase (PARP) inhibition. To recapitulate this effect with a small molecule, we ...

    Cyclin-dependent kinase (CDK) 12 knockdown via siRNA decreases the transcription of DNA-damage-response genes and sensitizes BRCA wild-type cells to poly(ADP-ribose) polymerase (PARP) inhibition. To recapitulate this effect with a small molecule, we sought a potent, selective CDK12 inhibitor. Crystal structures and modeling informed hybridization between dinaciclib and SR-3029, resulting in lead compound 5 [(S)-2-(1-(6-(((6,7-difluoro-1H-benzo[d]imidazol-2-yl)methyl)amino)-9-ethyl-9H-purin-2-yl)piperidin-2-yl)ethan-1-ol]. Further structure-guided optimization delivered a series of selective CDK12 inhibitors, including compound 7 [(S)-2-(1-(6-(((6,7-difluoro-1H-benzo[d]imidazol-2-yl)methyl)amino)-9-isopropyl-9H-purin-2-yl)piperidin-2-yl)ethan-1-ol]. Profiling of this compound across CDK9, 7, 2, and 1 at high ATP concentration, single-point kinase panel screening against 352 targets at 0.1 μm, and proteomics via kinase affinity matrix technology demonstrated the selectivity. This series of compounds inhibits phosphorylation of Ser2 on the C-terminal repeat domain of RNA polymerase II, consistent with CDK12 inhibition. These selective compounds were also acutely toxic to OV90 as well as THP1 cells.


    Organizational Affiliation

    Pharmaron Beijing Co. Ltd., 6 Taihe Road BDA, Beijing, 100176, P.R. China.,Discovery Sciences, IMED Biotech Unit, AstraZeneca Pharmaceuticals LP, Alderley Park, Macclesfield, SK10 4TG, UK.,Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA.,Oncology, IMED Biotech Unit, AstraZeneca, Boston, MA, USA.,Discovery Sciences, IMED Biotech Unit, AstraZeneca Pharmaceuticals LP, Unit 310 Darwin Building, Cambridge, CB4 0WG, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 12
A, C
320Homo 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
267Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CJM
Query on CJM

Download SDF File 
Download CCD File 
A, C
2-[(2S)-1-(6-{[(4,5-difluoro-1H-benzimidazol-2-yl)methyl]amino}-9-ethyl-9H-purin-2-yl)piperidin-2-yl]ethan-1-ol
C22 H26 F2 N8 O
HVFVQLFPRQYJTR-ZDUSSCGKSA-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: 3.06 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.190 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.140α = 76.53
b = 77.260β = 85.28
c = 90.640γ = 78.22
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-09-21 
  • Released Date: 2017-12-27 
  • Deposition Author(s): Ferguson, A.D.

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-03
    Type: Database references
  • Version 1.2: 2018-02-14
    Type: Database references
  • Version 1.3: 2018-02-21
    Type: Database references