Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68778.23 
• Atom Count: 4633 
• Residue Count: 591 
• Unique protein chains: 2

4BCG

Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor

• DOI: 10.2210/pdb4BCG/pdb

• Classification: TRANSFERASE/CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): 3 


• Deposited: 2012-10-02 Released: 2013-04-17 
• Deposition Author(s): Hole, A.J., Baumli, S., Wang, S., Endicott, J.A., Noble, M.E.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.085 Å
• R-Value Free: 0.197 
• R-Value Work: 0.161 

Literature

Substituted 4-(Thiazol-5-Yl)-2-(Phenylamino)Pyrimidines are Highly Active Cdk9 Inhibitors: Synthesis, X-Ray Crystal Structure, Sar and Anti-Cancer Activities.

Shao, H., Shi, S., Huang, S., Hole, A., Abbas, A.Y., Baumli, S., Liu, X., Lam, F., Foley, D.W., Fischer, P.M., Noble, M., Endicott, J.A., Pepper, C., Wang, S.

(2013) J.Med.Chem. 56: 640

• PubMed: 23301767 
• DOI: 10.1021/jm301475f
• Primary Citation of Related Structures:  
  4BCP


• PubMed Abstract: 
  

Cancer cells often have a high demand for antiapoptotic proteins in order to resist programmed cell death. CDK9 inhibition selectively targets survival proteins and reinstates apoptosis in cancer cells. We designed a series of 4-thiazol-2-anilinopyrimidine derivatives with functional groups attached to the C5-position of the pyrimidine or to the C4-thiazol moiety and investigated their effects on CDK9 potency and selectivity. One of the most selective compounds, 12u inhibits CDK9 with IC(50) = 7 nM and shows over 80-fold selectivity for CDK9 versus CDK2. X-ray crystal structures of 12u bound to CDK9 and CDK2 provide insights into the binding modes. This work, together with crystal structures of selected inhibitors in complex with both enzymes described in a companion paper, (34) provides a rationale for the observed SAR. 12u demonstrates potent anticancer activity against primary chronic lymphocytic leukemia cells with a therapeutic window 31- and 107-fold over those of normal B- and T-cells.

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Organizational Affiliation: 

School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CYCLIN-DEPENDENT KINASE 9	A	331	Homo sapiens	Mutation(s): 0  Gene Names: CDK9 (CDC2L4, TAK) EC: 2.7.11.22, 2.7.11.23
Find proteins for P50750 (Homo sapiens) Go to Gene View: CDK9 Go to UniProtKB:  P50750

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
CYCLIN-T1	B	260	Homo sapiens	Mutation(s): 3  Gene Names: CCNT1
Find proteins for O60563 (Homo sapiens) Go to Gene View: CCNT1 Go to UniProtKB:  O60563

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
T3C	A	2-[[3-(1,4-diazepan-1-yl)phenyl]amino]-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile C21 H24 N8 S BKOYUSKBPMSUBK-UHFFFAOYSA-N
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
T3C	Ki: 7 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.085 Å
• R-Value Free: 0.197 
• R-Value Work: 0.161 
• Space Group: H 3

Unit Cell:

Length (Å)	Angle (°)
a = 172.800	α = 90.00
b = 172.800	β = 90.00
c = 98.880	γ = 120.00

Software Package:

Software Name	Purpose
PHENIX	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-02 
• Released Date: 2013-04-17 
• Deposition Author(s): Hole, A.J., Baumli, S., Wang, S., Endicott, J.A., Noble, M.E.M.

Revision History 

• Version 1.0: 2013-04-17
  Type: Initial release