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)

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 129.00 kDa 
• Atom Count: 9118 
• Modelled Residue Count: 1114 
• Deposited Residue Count: 1123 
• Unique protein chains: 3

2X1N

Truncation and Optimisation of Peptide Inhibitors of CDK2, Cyclin A Through Structure Guided Design

• PDB DOI: 10.2210/pdb2X1N/pdb
• Entry: 2X1N supersedes: 2WHA

• Classification: CELL CYCLE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-31 Released: 2010-02-16 
• Deposition Author(s): Kontopidis, G., Andrews, M.J., McInnes, C., Plater, A., Innes, L., Renachowski, S., Cowan, A., Fischer, P.M., McIntyre, N.A., Griffiths, G., Barnett, A.L., Slawin, A.M.Z., Jackson, W., Thomas, M., Zheleva, D.I., Wang, S., Blake, D.G., Westwood, N.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.255 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Literature

Design, Synthesis, and Evaluation of 2-Methyl- and 2-Amino-N-Aryl-4,5-Dihydrothiazolo[4,5-H]Quinazolin-8-Amines as Ring-Constrained 2-Anilino-4-(Thiazol-5-Yl)Pyrimidine Cyclin-Dependent Kinase Inhibitors.

Mcintyre, N.A., Mcinnes, C., Griffiths, G., Barnett, A.L., Kontopidis, G., Slawin, A.M.Z., Jackson, W., Thomas, M., Zheleva, D.I., Wang, S., Blake, D.G., Westwood, N.J., Fischer, P.M.

(2010) J Med Chem 53: 2136

• PubMed: 20146435 
• DOI: 10.1021/jm901660c
• Primary Citation of Related Structures:  
  2X1N


• PubMed Abstract: 
  

Following the recent discovery and development of 2-anilino-4-(thiazol-5-yl)pyrimidine cyclin dependent kinase (CDK) inhibitors, a program was initiated to evaluate related ring-constrained analogues, specifically, 2-methyl- and 2-amino-N-aryl-4,5-dihydrothiazolo[4,5-h]quinazolin-8-amines for inhibition of CDKs. Here we report the rational design, synthesis, structure-activity relationships (SARs), and cellular mode-of-action profile of these second generation CDK inhibitors. Many of the analogues from this chemical series inhibit CDKs with very low nanomolar K(i) values. The most potent compound reported in this study inhibits CDK2 with an IC(50) of 0.7 nM ([ATP] = 100 microM). Furthermore, an X-ray crystal structure of 2-methyl-N-(3-(nitro)phenyl)-4,5-dihydrothiazolo[4,5-h]quinazolin-8-amine (11g), a representative from the chemical series in complex with cyclin A-CDK2, is reported, confirming the design rationale and expected binding mode within the CDK2 ATP binding pocket.

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Related Citations: 

• Truncation and Optimisation of Peptide Inhibitors of Cyclin-Dependent Kinase 2-Cyclin a Through Structure-Guided Design.
  Kontopidis, G., Andrews, M.J., Mcinnes, C., Plater, A., Innes, L., Renachowski, S., Cowan, A., Fischer, P.M.
  (2009) ChemMedChem 4: 1120

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Organizational Affiliation: 

School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 2	A, C	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941 GTEx:  ENSG00000123374

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN-A2	B, D	261	Homo sapiens	Mutation(s): 0  Gene Names: CCNA2, CCN1, CCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens) Explore P20248  Go to UniProtKB:  P20248
PHAROS:  P20248 GTEx:  ENSG00000145386

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-LEU-ASN-PFF-NH2	E [auth H]	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X1N	F [auth A], G [auth C]	2-METHYL-N-[(1Z)-3-NITROCYCLOHEXA-2,4-DIEN-1-YLIDENE]-4,5-DIHYDRO[1,3]THIAZOLO[4,5-H]QUINAZOLIN-8-AMINE C16 H13 N5 O2 S CMWWYSDXIZEJPA-ODLFYWEKSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PFF	E [auth H]	L-PEPTIDE LINKING	C9 H10 F N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.255 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.558	α = 90
b = 114.257	β = 90
c = 157.277	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-31 
• Released Date: 2010-02-16 
Deposition Author(s): Kontopidis, G., Andrews, M.J., McInnes, C., Plater, A., Innes, L., Renachowski, S., Cowan, A., Fischer, P.M., McIntyre, N.A., Griffiths, G., Barnett, A.L., Slawin, A.M.Z., Jackson, W., Thomas, M., Zheleva, D.I., Wang, S., Blake, D.G., Westwood, N.J.
• This entry supersedes: 2WHA

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2016-12-14
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-03-29
  Changes: Other