Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method

Table 1 CDK2 Inhibitor Data Set.

Entry	PDB	Resolution (Å)	IC₅₀ (μM)	$Δ G_{\underset{E x p t}{b i n d}}$
1^a	2VTA	2	185.000	-5.292
2^a	2VTH	1.9	120.000	-5.558
3^a	2VTM	2.25	1000.000	-4.253
4	2VTJ^b		7.000	-7.308
5^a	2VTJ	2.2	1.900	-8.110
6^a	2VTR	1.9	1.500	-8.256
7^a	2VTS	1.9	0.030	-10.665
8	2VTN^b		3.000	-7.829
9^a	2VTI	2	0.660	-8.761
10^a	2VTL	2	97.000	-5.689
11	2VTN^b		25.000	-6.524
12	2VTN^b		85.000	-5.770
13^a	2VTN	2.2	0.850	-8.606
14	2VTP^b		0.730	-8.699
15	2VTT^b		1.600	-8.216
16	2VTT^b		0.090	-9.988
17^a	2VTO	2.19	0.140	-9.716
18^a	2VTP	2.15	0.003	-12.082
19	2VTT^b		0.025	-10.777
20	2VTT^b		0.012	-11.229
21	2VTT^b		0.019	-10.946
22	2VTT^b		0.038	-10.519
23^a	2VTQ	1.9	0.140	-9.716
24^a	2VTT	1.68	0.044	-10.429
25	2VTT^b		0.910	-8.564
26	2VTT^b		0.052	-10.326
27	2VTT^b		0.063	-10.208
28^a	2VU3	1.85	0.082	-10.045

Structures of the small molecule CDK2 inhibitors are shown, together with the reference PDB structure from which the compound was extracted, the resolution (Å) of the PDB structure, the ligand potency (IC₅₀ in μM) and the experimental free energy of binding (kcal/mol). a) Entries which made up the training sets for each of the MM and QM methods used to estimate the free energy of binding; b) the reference PDB structure used in the modelling the protein-ligand complex where an experimentally determined X-ray structure was not available.

ISSN: 1758-2946