Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 68.78 kDa 
• Atom Count: 4649 
• Modelled Residue Count: 565 
• Deposited Residue Count: 591 
• Unique protein chains: 2

4BCG

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

• PDB DOI: 10.2210/pdb4BCG/pdb

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


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 0.197 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

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:  
  4BCG, 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.

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN-DEPENDENT KINASE 9	A	331	Homo sapiens	Mutation(s): 0  Gene Names: CDK9, CDC2L4, TAK 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN-T1	B	260	Homo sapiens	Mutation(s): 3  Gene Names: CCNT1
UniProt & NIH Common Fund Data Resources
Find proteins for O60563 (Homo sapiens) Explore O60563  Go to UniProtKB:  O60563
PHAROS:  O60563

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T3C	C [auth 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	D [auth A], E [auth B]	GLYCEROL 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

Binding Affinity Annotations
ID	Source	Binding Affinity
T3C	BindingDB:  4BCG	Ki: 7 (nM) from 1 assay(s)
		IC50: 14 (nM) from 1 assay(s)
	PDBBind:  4BCG	Ki: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 0.197 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.8	α = 90
b = 172.8	β = 90
c = 98.88	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	phasing

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
  
• Version 1.1: 2019-05-15
  Changes: Data collection, Derived calculations, Experimental preparation, Other