6GZM | pdb_00006gzm

Crystal Structure of Human CKIdelta with A86


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.250 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Small Molecules Co-targeting CKI alpha and the Transcriptional Kinases CDK7/9 Control AML in Preclinical Models.

Minzel, W.Venkatachalam, A.Fink, A.Hung, E.Brachya, G.Burstain, I.Shaham, M.Rivlin, A.Omer, I.Zinger, A.Elias, S.Winter, E.Erdman, P.E.Sullivan, R.W.Fung, L.Mercurio, F.Li, D.Vacca, J.Kaushansky, N.Shlush, L.Oren, M.Levine, R.Pikarsky, E.Snir-Alkalay, I.Ben-Neriah, Y.

(2018) Cell 175: 171-185.e25

  • DOI: https://doi.org/10.1016/j.cell.2018.07.045
  • Primary Citation Related Structures: 
    6GZD, 6GZH, 6GZM

  • PubMed Abstract: 

    CKIα ablation induces p53 activation, and CKIα degradation underlies the therapeutic effect of lenalidomide in a pre-leukemia syndrome. Here we describe the development of CKIα inhibitors, which co-target the transcriptional kinases CDK7 and CDK9, thereby augmenting CKIα-induced p53 activation and its anti-leukemic activity. Oncogene-driving super-enhancers (SEs) are highly sensitive to CDK7/9 inhibition. We identified multiple newly gained SEs in primary mouse acute myeloid leukemia (AML) cells and demonstrate that the inhibitors abolish many SEs and preferentially suppress the transcription elongation of SE-driven oncogenes. We show that blocking CKIα together with CDK7 and/or CDK9 synergistically stabilize p53, deprive leukemia cells of survival and proliferation-maintaining SE-driven oncogenes, and induce apoptosis. Leukemia progenitors are selectively eliminated by the inhibitors, explaining their therapeutic efficacy with preserved hematopoiesis and leukemia cure potential; they eradicate leukemia in MLL-AF9 and Tet2 -/- ;Flt3 ITD AML mouse models and in several patient-derived AML xenograft models, supporting their potential efficacy in curing human leukemia.


  • Organizational Affiliation
    • The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.

Macromolecule Content 

  • Total Structure Weight: 69.87 kDa 
  • Atom Count: 6,063 
  • Modeled Residue Count: 586 
  • Deposited Residue Count: 590 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Casein kinase I isoform delta
A, B
295Homo sapiensMutation(s): 1 
Gene Names: CSNK1DHCKID
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P48730 (Homo sapiens)
Explore P48730 
Go to UniProtKB:  P48730
PHAROS:  P48730
GTEx:  ENSG00000141551 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48730
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.250 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.232α = 90
b = 73.659β = 103.57
c = 89.204γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description