6Z45

CDK9-Cyclin-T1 complex bound by compound 24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of AZD4573, a Potent and Selective Inhibitor of CDK9 That Enables Short Duration of Target Engagement for the Treatment of Hematological Malignancies.

Barlaam, B.Casella, R.Cidado, J.Cook, C.De Savi, C.Dishington, A.Donald, C.S.Drew, L.Ferguson, A.D.Ferguson, D.Glossop, S.Grebe, T.Gu, C.Hande, S.Hawkins, J.Hird, A.W.Holmes, J.Horstick, J.Jiang, Y.Lamb, M.L.McGuire, T.M.Moore, J.E.O'Connell, N.Pike, A.Pike, K.G.Proia, T.Roberts, B.San Martin, M.Sarkar, U.Shao, W.Stead, D.Sumner, N.Thakur, K.Vasbinder, M.M.Varnes, J.G.Wang, J.Wang, L.Wu, D.Wu, L.Yang, B.Yao, T.

(2020) J Med Chem 63: 15564-15590

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01754
  • Primary Citation of Related Structures:  
    6Z45

  • PubMed Abstract: 

    A CDK9 inhibitor having short target engagement would enable a reduction of Mcl-1 activity, resulting in apoptosis in cancer cells dependent on Mcl-1 for survival. We report the optimization of a series of amidopyridines (from compound 2 ), focusing on properties suitable for achieving short target engagement after intravenous administration. By increasing potency and human metabolic clearance, we identified compound 24 , a potent and selective CDK9 inhibitor with suitable predicted human pharmacokinetic properties to deliver transient inhibition of CDK9. Furthermore, the solubility of 24 was considered adequate to allow i.v. formulation at the anticipated effective dose. Short-term treatment with compound 24 led to a rapid dose- and time-dependent decrease of pSer2-RNAP2 and Mcl-1, resulting in cell apoptosis in multiple hematological cancer cell lines. Intermittent dosing of compound 24 demonstrated efficacy in xenograft models derived from multiple hematological tumors. Compound 24 is currently in clinical trials for the treatment of hematological malignancies.


  • Organizational Affiliation

    Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 9330Homo sapiensMutation(s): 0 
Gene Names: CDK9CDC2L4TAK
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P50750 (Homo sapiens)
Explore P50750 
Go to UniProtKB:  P50750
PHAROS:  P50750
GTEx:  ENSG00000136807 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50750
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-T1258Homo sapiensMutation(s): 0 
Gene Names: CCNT1
UniProt & NIH Common Fund Data Resources
Find proteins for O60563 (Homo sapiens)
Explore O60563 
Go to UniProtKB:  O60563
PHAROS:  O60563
GTEx:  ENSG00000129315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60563
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q6E (Subject of Investigation/LOI)
Query on Q6E

Download Ideal Coordinates CCD File 
C [auth A](1~{S},3~{R})-3-acetamido-~{N}-[5-chloranyl-4-(5,5-dimethyl-4,6-dihydropyrrolo[1,2-b]pyrazol-3-yl)pyridin-2-yl]cyclohexane-1-carboxamide
C22 H28 Cl N5 O2
AVIWDYSJSPOOAR-LSDHHAIUSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
Q6E BindingDB:  6Z45 Kd: min: 0.09, max: 711 (nM) from 2 assay(s)
IC50: min: 3, max: 3000 (nM) from 4 assay(s)
EC50: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.76α = 90
b = 171.76β = 90
c = 97.79γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-01-06
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary