6GZD | pdb_00006gzd

Crystal structure of Human CSNK1A1 with A86


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.221 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6GZD

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: 45.22 kDa 
  • Atom Count: 2,865 
  • Modeled Residue Count: 297 
  • Deposited Residue Count: 374 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Casein kinase I isoform alpha374Homo sapiensMutation(s): 0 
Gene Names: CSNK1A1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P48729 (Homo sapiens)
Explore P48729 
Go to UniProtKB:  P48729
PHAROS:  P48729
GTEx:  ENSG00000113712 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48729
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LCI

Query on LCI



Download:Ideal Coordinates CCD File
S [auth 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
TCE

Query on TCE



Download:Ideal Coordinates CCD File
R [auth A]3,3',3''-phosphanetriyltripropanoic acid
C9 H15 O6 P
PZBFGYYEXUXCOF-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
L [auth A]
M [auth A]
N [auth A]
O [auth A]
P [auth A]
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.221 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.383α = 90
b = 113.383β = 90
c = 80.878γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
REFMACphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report



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