Selective anticancer activity of a hexapeptide with sequence homology to a non-kinase domain of Cyclin Dependent Kinase 4

Table 1 Quality and accuracy scores for the built models

MODEL	Model 1	Model 2	Model 3	Model 4	Model 5
Template	1BLX (CDK6)	1G3N (CDK6)	Base template 1BLX, Variable regions differing by more than 2.0 Å rmsd modelled from 1G3N, 1BI8, 1BI7 and 1JOW (all CDK6)	Base template 1BLX, Variable regions differing by more than 2.0 Å rmsd. modelled from 1HCL (CDK2)	Base template 1BLX, Variable regions differing by more than 2.0 Å rmsd. modelled from 1GII (CDK2)
Threading score	165.6	158.2	151.0	128.8	99.7
Molecular mechanics energy (kJ mol^-1)	-12203.3	-12526.1	-12182.5	-11900.3	-11795.5
RMS deviation from 1BLX (in Å)	0.48	0.88	0.62	0.67	0.65
Structure Z-scores, positive is better than average
2^nd generation packing quality	-1.093	-0.868	-0.964	-1.090	-1.228
Ramachandran plot appearance	-2.573	-3.374	-2.837	-2.965	-3.104
χ-1/χ-2 rotamer quality	-1.148	-1.470	-1.340	-0.955	-0.968
Backbone conformation	-6.485	-5.201	-5.637	-7.016	-7.564
RMS Z-scores,should be close to 1
Bond lengths	0.655	0.645	0.652	0.657	0.668
Bond angles	1.187	1.176	1.183	1.168	1.181
Omega angle restraints	1.354	1.159	1.413	1.478	1.396
Side chain planarity	1.608	1.667	1.494	1.277	1.292
Improper dihedral distribution	0.883	0.882	0.907	0.879	0.865
Inside/Outside distribution	1.019	1.038	1.025	1.043	1.051

A high threading score indicates a better fit of the sequence in the structure. A low molecular mechanics energy indicates a more relaxed structure.
Structural Z-scores less than -2.0 indicate problems in the model, scores less then -4.0 indicates serious errors. RMS Z-scores should be close to 1.0.

ISSN: 1476-4598