5ACB

Crystal Structure of the Human Cdk12-Cyclink Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Covalent Targeting of Remote Cysteine Residues to Develop Cdk12 and Cdk13 Inhibitors.

Zhang, T.Kwiatkowski, N.Olson, C.M.Dixon-Clarke, S.E.Abraham, B.J.Greifenberg, A.K.Ficarro, S.B.Elkins, J.M.Liang, Y.Hannett, N.M.Manz, T.Hao, M.Bartkowiak, B.Greenleaf, A.L.Marto, J.A.Geyer, M.Bullock, A.N.Young, R.A.Gray, N.S.

(2016) Nat.Chem.Biol. 12: 876

  • DOI: 10.1038/nchembio.2166

  • PubMed Abstract: 
  • Cyclin-dependent kinases 12 and 13 (CDK12 and CDK13) play critical roles in the regulation of gene transcription. However, the absence of CDK12 and CDK13 inhibitors has hindered the ability to investigate the consequences of their inhibition in healt ...

    Cyclin-dependent kinases 12 and 13 (CDK12 and CDK13) play critical roles in the regulation of gene transcription. However, the absence of CDK12 and CDK13 inhibitors has hindered the ability to investigate the consequences of their inhibition in healthy cells and cancer cells. Here we describe the rational design of a first-in-class CDK12 and CDK13 covalent inhibitor, THZ531. Co-crystallization of THZ531 with CDK12-cyclin K indicates that THZ531 irreversibly targets a cysteine located outside the kinase domain. THZ531 causes a loss of gene expression with concurrent loss of elongating and hyperphosphorylated RNA polymerase II. In particular, THZ531 substantially decreases the expression of DNA damage response genes and key super-enhancer-associated transcription factor genes. Coincident with transcriptional perturbation, THZ531 dramatically induced apoptotic cell death. Small molecules capable of specifically targeting CDK12 and CDK13 may thus help identify cancer subtypes that are particularly dependent on their kinase activities.


    Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-K
A, B
259Homo sapiensMutation(s): 0 
Gene Names: CCNK (CPR4)
Find proteins for O75909 (Homo sapiens)
Go to Gene View: CCNK
Go to UniProtKB:  O75909
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-DEPENDENT KINASE 12
C, D
340Homo 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5I1
Query on 5I1

Download SDF File 
Download CCD File 
C, D
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
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
C, D
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.780α = 90.00
b = 148.690β = 93.81
c = 91.580γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2016-08-31
    Type: Database references
  • Version 1.2: 2016-09-21
    Type: Database references
  • Version 1.3: 2016-10-05
    Type: Database references