3VS3

Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo

Saito, Y.Yuki, H.Kuratani, M.Hashizume, Y.Takagi, S.Honma, T.Tanaka, A.Shirouzu, M.Mikuni, J.Handa, N.Ogahara, I.Sone, A.Najima, Y.Tomabechi, Y.Wakiyama, M.Uchida, N.Tomizawa-Murasawa, M.Kaneko, A.Tanaka, S.Suzuki, N.Kajita, H.Aoki, Y.Ohara, O.Shultz, L.D.Fukami, T.Goto, T.Taniguchi, S.Yokoyama, S.Ishikawa, F.

(2013) Sci Transl Med 5: 181ra52-181ra52

  • DOI: https://doi.org/10.1126/scitranslmed.3004387
  • Primary Citation of Related Structures:  
    3VRY, 3VRZ, 3VS0, 3VS1, 3VS2, 3VS3, 3VS4, 3VS5, 3VS6, 3VS7

  • PubMed Abstract: 

    Leukemia stem cells (LSCs) that survive conventional chemotherapy are thought to contribute to disease relapse, leading to poor long-term outcomes for patients with acute myeloid leukemia (AML). We previously identified a Src-family kinase (SFK) member, hematopoietic cell kinase (HCK), as a molecular target that is highly differentially expressed in human primary LSCs compared with human normal hematopoietic stem cells (HSCs). We performed a large-scale chemical library screen that integrated a high-throughput enzyme inhibition assay, in silico binding prediction, and crystal structure determination and found a candidate HCK inhibitor, RK-20449, a pyrrolo-pyrimidine derivative with an enzymatic IC50 (half maximal inhibitory concentration) in the subnanomolar range. A crystal structure revealed that RK-20449 bound the activation pocket of HCK. In vivo administration of RK-20449 to nonobese diabetic (NOD)/severe combined immunodeficient (SCID)/IL2rg(null) mice engrafted with highly aggressive therapy-resistant AML significantly reduced human LSC and non-stem AML burden. By eliminating chemotherapy-resistant LSCs, RK-20449 may help to prevent relapse and lead to improved patient outcomes in AML.


  • Organizational Affiliation

    Laboratory for Human Disease Models, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase HCK
A, B
454Homo sapiensMutation(s): 3 
Gene Names: HCK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P08631 (Homo sapiens)
Explore P08631 
Go to UniProtKB:  P08631
GTEx:  ENSG00000101336 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08631
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
VSE BindingDB:  3VS3 IC50: min: 0.4, max: 0.43 (nM) from 3 assay(s)
PDBBind:  3VS3 IC50: 0.43 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.45α = 90
b = 73.592β = 96.3
c = 180.712γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2023-12-06
    Changes: Data collection