4TTH

Crystal structure of a CDK6/Vcyclin complex with inhibitor bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4P41


Literature

Discovery of AMG 925, a FLT3 and CDK4 dual kinase inhibitor with preferential affinity for the activated state of FLT3.

Li, Z.Wang, X.Eksterowicz, J.Gribble, M.W.Alba, G.Q.Ayres, M.Carlson, T.J.Chen, A.Chen, X.Cho, R.Connors, R.V.DeGraffenreid, M.Deignan, J.T.Duquette, J.Fan, P.Fisher, B.Fu, J.Huard, J.N.Kaizerman, J.Keegan, K.S.Li, C.Li, K.Li, Y.Liang, L.Liu, W.Lively, S.E.Lo, M.C.Ma, J.McMinn, D.L.Mihalic, J.T.Modi, K.Ngo, R.Pattabiraman, K.Piper, D.E.Queva, C.Ragains, M.L.Suchomel, J.Thibault, S.Walker, N.Wang, X.Wang, Z.Wanska, M.Wehn, P.M.Weidner, M.F.Zhang, A.J.Zhao, X.Kamb, A.Wickramasinghe, D.Dai, K.McGee, L.R.Medina, J.C.

(2014) J Med Chem 57: 3430-3449

  • DOI: https://doi.org/10.1021/jm500118j
  • Primary Citation of Related Structures:  
    4TTH

  • PubMed Abstract: 

    We describe the structural optimization of a lead compound 1 that exhibits dual inhibitory activities against FLT3 and CDK4. A series of pyrido[4',3':4,5]pyrrolo[2,3-d]pyrimidine derivatives was synthesized, and SAR analysis, using cell-based assays, led to the discovery of 28 (AMG 925), a potent and orally bioavailable dual inhibitor of CDK4 and FLT3, including many FLT3 mutants reported to date. Compound 28 inhibits the proliferation of a panel of human tumor cell lines including Colo205 (Rb(+)) and U937 (FLT3(WT)) and induced cell death in MOLM13 (FLT3(ITD)) and even in MOLM13 (FLT3(ITD, D835Y)), which exhibits resistance to a number of FLT3 inhibitors currently under clinical development. At well-tolerated doses, compound 28 leads to significant growth inhibition of MOLM13 xenografts in nude mice, and the activity correlates with inhibition of STAT5 and Rb phosphorylation.


  • Organizational Affiliation

    Departments of †Therapeutic Discovery, ‡Oncology Research, §Pharmaceutics, and ∥Pharmacokinetics and Drug Metabolism, Amgen Inc. , 1120 Veterans Boulevard, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin homolog254Herpesvirus saimiri (strain 11)Mutation(s): 0 
Gene Names: 72ECLF2
UniProt
Find proteins for Q01043 (Saimiriine herpesvirus 2 (strain 11))
Explore Q01043 
Go to UniProtKB:  Q01043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01043
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 6326Homo sapiensMutation(s): 0 
Gene Names: CDK6CDKN6
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q00534 (Homo sapiens)
Explore Q00534 
Go to UniProtKB:  Q00534
PHAROS:  Q00534
GTEx:  ENSG00000105810 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00534
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
24V
Query on 24V

Download Ideal Coordinates CCD File 
C [auth B]9-cyclopentyl-N-(5-piperazin-1-ylpyridin-2-yl)pyrido[4,5]pyrrolo[1,2-d]pyrimidin-2-amine
C23 H26 N8
MCPPMOSBWNMSOA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
24V BindingDB:  4TTH IC50: 4.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.1α = 90
b = 71.1β = 90
c = 448.995γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Aimlessdata 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: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description