4TTH

Crystal structure of a CDK6/Vcyclin complex with inhibitor bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

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

  • 4P41 - determined by Piper, D.E., Walker, N., Wang, Z.  

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: 10.1021/jm500118j
  • Primary Citation of Related Structures:  4P41

  • 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, ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin homolog
A
254Saimiriine herpesvirus 2 (strain 11)Gene Names: 72 (ECLF2)
Find proteins for Q01043 (Saimiriine herpesvirus 2 (strain 11))
Go to UniProtKB:  Q01043
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 6
B
326Homo sapiensGene Names: CDK6 (CDKN6)
EC: 2.7.11.22
Find proteins for Q00534 (Homo sapiens)
Go to Gene View: CDK6
Go to UniProtKB:  Q00534
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
24V
Query on 24V

Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
24VIC50: 4.4 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.235 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.100α = 90.00
b = 71.100β = 90.00
c = 448.995γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Derived calculations, Other, Refinement description, Source and taxonomy