6GZD

Crystal structure of Human CSNK1A1 with A86


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.cell.2018.07.045
  • Primary Citation of Related Structures:  

  • 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, th ...

    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; Department of Hematology, Hadassah Medical Center, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel; Department of Pathology, Hadassah Medical Center, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,WuXi AppTec, Shanghai, China.,The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Bioinformatics Unit of the I-CORE Computation Center, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,BioTheryX Inc., San Diego, CA, USA.,Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel.,The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel. Electronic address: yinonb@ekmd.huji.ac.il.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase I isoform alpha
A
374Homo sapiensMutation(s): 0 
Gene Names: CSNK1A1
EC: 2.7.11.1
Find proteins for P48729 (Homo sapiens)
Go to Gene View: CSNK1A1
Go to UniProtKB:  P48729
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

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

Download SDF File 
Download CCD File 
A
[4-[[4-[5-(cyclopropylmethyl)-1-methyl-pyrazol-4-yl]-5-fluoranyl-pyrimidin-2-yl]amino]cyclohexyl]azanium
C18 H26 F N6
YSPIHUWHLMNFOV-JOCQHMNTSA-O
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
TCE
Query on TCE

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Download CCD File 
A
3,3',3''-phosphanetriyltripropanoic acid
3-[bis(2-carboxyethyl)phosphanyl]propanoic acid
C9 H15 O6 P
PZBFGYYEXUXCOF-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 113.383α = 90.00
b = 113.383β = 90.00
c = 80.878γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-05
    Type: Data collection, Database references
  • Version 1.2: 2018-10-03
    Type: Data collection, Database references