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. Author manuscript; available in PMC: 2010 Jul 2.
Published in final edited form as: Proteins. 2007 Nov 1;69(2):326–339. doi: 10.1002/prot.21500

Table I.

Structures, Inhibitory Potencies, and Simulation Data for Studied Inhibitors of MMP-3.

graphic file with name nihms83443t1.jpg
No X R1 R2 log(1/Ki) Linear Response terms in Steps 3 and 4 −Δ<x>, E in kcal/mol and SASA in Å2 SD a Bond length (Å) Angle b
Exp. Calc. EvdW Eel EQM/MM. SASA O1-Zn O2-Zn O1-Zn-N2 O1-Zn-N3 N2-Zn-N3
1 X1 CH2CH3 graphic file with name nihms83443t2.jpg 8.284 8.200 11.609 50.30 1890.75 464.46 0.155 1.844 2.017 104.6 167.5 87.9
2 X1 CH3 graphic file with name nihms83443t3.jpg 8.530 8.279 388.912 90.60 1924.28 477.20 0.765 1.956 1.947 104.9 166.3 88.8
3 X1 graphic file with name nihms83443t4.jpg graphic file with name nihms83443t5.jpg 8.285 7.986 178.393 34.05 1863.53 428.70 0.456 1.946 1.948 94.8 179.0 84.3
4 X1 graphic file with name nihms83443t6.jpg graphic file with name nihms83443t7.jpg 8.614 8.383 20.535 32.80 2067.29 491.82 0.213 1.965 1.953 108.0 164.1 86.9
5 X1 graphic file with name nihms83443t8.jpg graphic file with name nihms83443t9.jpg 7.893 7.963 45.864 89.39 2493.80 411.07 0.318 1.947 1.947 100.6 171.4 87.8
6 X1 (CH2)2N(CH2CH3)2 graphic file with name nihms83443t10.jpg 7.084 7.544 176.487 19.79 917.12 373.92 0.143 1.716 1.931 135.0 119.2 104.3
7 X1 graphic file with name nihms83443t11.jpg graphic file with name nihms83443t12.jpg 8.193 7.915 58.753 107.98 4776.15 353.47 0.202 1.849 2.031 102.1 164.8 91.2
8 X1 (CH2)2OCH2CH3 graphic file with name nihms83443t13.jpg 8.265 8.314 80.24 60.85 4873.99 419.29 0.322 1.947 1.943 103.9 161.6 91.1
9 X1 CH2CH3 graphic file with name nihms83443t14.jpg 7.457 7.342 20.15 11.66 1720.62 322.14 0.26 1.946 1.946 106.6 167.2 86.6
10 X1 CH2CH3 graphic file with name nihms83443t15.jpg 7.137 7.373 354.63 38.08 741.11 348.69 0.438 1.843 2.017 105.3 161.9 89.7
11 X1 CH2CH3 graphic file with name nihms83443t16.jpg 7.191 7.229 40.65 78.51 717.76 324.64 0.314 1.874 2.017 110.8 161.5 86.9
12 X1 CH2CH3 graphic file with name nihms83443t17.jpg 7.289 7.235 199.06 82.27 1341.75 312.27 0.743 1.867 1.987 115.2 153.8 90.3
13 X1 CH2CH3 graphic file with name nihms83443t18.jpg 7.321 7.397 193.55 20.27 1659.06 332.94 0.395 1.875 1.99 104.5 167.8 85.7
14 X1 CH2CH3 graphic file with name nihms83443t19.jpg 6.721 7.089 11.25 82.37 366.37 308.51 0.393 1.846 2.017 99.8 165 90.7
15 X1 CH2CH3 graphic file with name nihms83443t20.jpg 6.790 7.035 352.53 57.27 482.85 296.74 0.112 1.866 1.988 113.3 152.9 93.5
16 X1 CH2CH3 graphic file with name nihms83443t21.jpg 7.174 7.131 15.46 93.94 910.25 303.89 0.246 1.797 2.071 115.0 154.3 90.4
17 X1 CH2CH3 graphic file with name nihms83443t22.jpg 7.529 7.382 51.40 27.01 957.79 345.61 0.541 1.81 1.593 137.4 130.7 91.9
18 X1 CH2CH3 graphic file with name nihms83443t23.jpg 8.361 8.555 71.37 60.94 7570.98 401.89 0.281 1.875 1.995 119.3 150.4 89.7
19 X1 CH2CH3 graphic file with name nihms83443t24.jpg 9.276 9.474 408.72 24.23 8665.43 534.54 0.101 1.849 2.026 124.0 142.8 93.2
20 X1 CH2CH3 graphic file with name nihms83443t25.jpg 8.314 8.089 30.33 46.60 1497.50 454.18 0.131 1.758 2.039 116.0 148.8 93.5
21 X1 CH2CH3 graphic file with name nihms83443t26.jpg 9.301 9.432 36.51 67.38 7988.86 542.06 0.106 1.86 2.015 107.7 161.4 89.6
22 X1 CH2CH3 graphic file with name nihms83443t27.jpg 7.936 7.545 46.63 135.80 3970.28 308.13 0.165 1.83 1.961 105.4 166.6 88.0
23 X2 CH2CH3 graphic file with name nihms83443t28.jpg 7.910 7.558 50.09 111.94 3283.05 325.14 0.17 1.864 1.988 94.7 163.6 84.1
24 X3 CH2CH3 graphic file with name nihms83443t29.jpg 8.284 8.062 41.45 13.68 4667.35 380.83 1.78 2.052 2.028 104.8 158.2 85.5
25 X4 CH2CH3 graphic file with name nihms83443t30.jpg 8.69 9.028 213.47 134.26 4963.11 538.76 0.399 1.821 1.875 125.2 130.7 101.1
26 X5 CH2CH3 graphic file with name nihms83443t31.jpg 7.827 7.871 22.22 33.22 1625.96 414.26 0.213 1.861 2.057 110.4 161.0 86.0
27 X6 CH2CH3 graphic file with name nihms83443t32.jpg 6.278 6.502 27.52 82.75 326.19 209.48 0.329 1.95 1.945 105.3 158.8 87.2
a

Standard deviation for the inhibitor atoms during the MD simulation.

b

Ideal values are 120° for trigonal bipyramid in all three cases, and 90°, 180°, and 90°, respectively, for the square pyramid. See Figure 1 for atom numbering.