5ACB

Crystal Structure of the Human Cdk12-Cyclink Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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
  • Primary Citation of Related Structures:  
    5ACB

  • 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 Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN-KAB259Homo sapiensMutation(s): 0 
Gene Names: CCNKCPR4
Find proteins for O75909 (Homo sapiens)
Explore O75909 
Go to UniProtKB:  O75909
NIH Common Fund Data Resources
PHAROS  O75909
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN-DEPENDENT KINASE 12CD340Homo sapiensMutation(s): 0 
Gene Names: CDK12CRK7CRKRSKIAA0904
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (UniProt)
Find proteins for Q9NYV4 (Homo sapiens)
Explore Q9NYV4 
Go to UniProtKB:  Q9NYV4
NIH Common Fund Data Resources
PHAROS  Q9NYV4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5I1
Query on 5I1

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,DL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.78α = 90
b = 148.69β = 93.81
c = 91.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

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