5ZXB

Crystal structure of ACK1 with compound 10d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

First SAR Study for Overriding NRAS Mutant Driven Acute Myeloid Leukemia.

Cho, H.Shin, I.Ju, E.Choi, S.Hur, W.Kim, H.Hong, E.Kim, N.D.Choi, H.G.Gray, N.S.Sim, T.

(2018) J Med Chem 61: 8353-8373

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00882
  • Primary Citation of Related Structures:  
    5ZXB

  • PubMed Abstract: 

    GNF-7, a multitargeted kinase inhibitor, served as a dual kinase inhibitor of ACK1 and GCK, which provided a novel therapeutic strategy for overriding AML expressing NRAS mutation. This SAR study with GNF-7 derivatives, designed to target NRAS mutant-driven AML, led to identification of the extremely potent inhibitors, 10d, 10g, and 11i, which possess single-digit nanomolar inhibitory activity against both ACK1 and GCK. These substances strongly suppress proliferation of mutant NRAS expressing AML cells via apoptosis and AKT/mTOR signaling blockade. Compound 11i is superior to GNF-7 in terms of kinase inhibitory activity, cellular activity, and differential cytotoxicity. Moreover, 10k possessing a favorable mouse pharmacokinetic profile prolonged life-span of Ba/F3-NRAS-G12D injected mice and significantly delayed tumor growth of OCI-AML3 xenograft model without causing the prominent level of toxicity found with GNF-7. Taken together, this study provides insight into the design of novel ACK1 and GCK dual inhibitors for overriding NRAS mutant-driven AML.


  • Organizational Affiliation

    KU-KIST Graduate School of Converging Science and Technology , Korea University , 145 Anam-ro, Seongbuk-gu , Seoul 02841 , Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Activated CDC42 kinase 1
A, B
275Homo sapiensMutation(s): 0 
Gene Names: TNK2ACK1
EC: 2.7.10.2 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q07912 (Homo sapiens)
Explore Q07912 
Go to UniProtKB:  Q07912
PHAROS:  Q07912
GTEx:  ENSG00000061938 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07912
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9KO (Subject of Investigation/LOI)
Query on 9KO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-{3-[7-{[6-(4-acetylpiperazin-1-yl)pyridin-3-yl]amino}-1-methyl-2-oxo-1,4-dihydropyrimido[4,5-d]pyrimidin-3(2H)-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide
C33 H32 F3 N9 O3
FCMNXGJPIJFWQV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9KO BindingDB:  5ZXB IC50: 8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.182α = 90
b = 43.12β = 98.34
c = 93.891γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Korea, Republic OfNRF-2016M3A9B5940991

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Refinement description, Structure summary