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. Author manuscript; available in PMC: 2009 Feb 27.
Published in final edited form as: J Comput Aided Mol Des. 2008 Sep 9;23(1):37–47. doi: 10.1007/s10822-008-9236-1

Table 1.

Structures and binding affinities of the fifteen compounds

graphic file with name nihms80668f8.jpg
Compound ChemDiv ID R1 R2 Exchange regimeb Δδc KDd (mM) KD’e (μM)
1 5435-0027 Aa -ph-4-CH3 -ph ++++ 0.411 0.98 8.6
2 3865-0097 A -ph -CH3 +++ 0.285 3.10 27.2
3 0277-0075 A -ph-4-N(CH2CH2Cl)2 -CH3 + 0.063 8.98 78.8
4 3865-0011 B1 -ph -ph ++ 0.204 5.67 49.8
5 3379-2711 B1 -ph-4-Cl -ph n/a 0.245 1.16 10.2
6 3802-0264 B1 -ph -ph-4-(OCH3) + 0.187 3.48 30.5
7 3865-0047 B1 -ph-4-F -ph + 0.142 5.09 44.7
8 5613-0298 B1 -ph-4-(OCH3) -ph-4-CH3 + 0.167 2.33 20.5
9 2509-0036 B1 -ph-4-Br -ph-3,4,5-3(OCH3) ++ 0.239 2.34 20.5
10 2509-0040 B1 -ph-3,5-2(OCH3) -ph-3,4,5-3(OCH3) +++ 0.188 2.46 21.6
11 5613-0343 B1 -5-benzo[d][1,3]dioxol -ph-4-CH3 + 0.208 1.59 14.0
12 3631-0149 B2 -ph -2-furan ++++ 0.206 2.58 22.6
13 3379-2681 B2 -ph-4-Cl -2-furan + 0.192 2.99 26.2
14 3379-2909 B2 -ph-4-F -2-furan + 0.170 4.28 37.6
15 3802-0137 B3 -2-(furan-3-Br) -2-furan + 0.175 4.47 39.2
NSC668036 + 0.035 27 237
a

Compounds labeled A have scaffold A and compounds labeled B1, B2, and B3 have scaffold B.

b

Compounds from being in intermediate exchange (++++) to fast exchange (+) with the PDZ domain. Compounds with “++++” caused some peaks disappear and reappear; compounds with “+++” caused peaks disappear only; compounds with “++” caused peaks become weak only; and compounds with “+” did not cause any peak intensity changes.

c

The chemical shift perturbation changes of Arg322 caused by 10 equivalents of compounds except for 10.8 equivalents of compound 1 and 10.4 equivalents of NSC668036.

d

KD (in mM) measured by NMR titration experiments at 25 °C.

e

KD (in μM) values were obtained by normalizing the KD values obtained in the NMR experiments with the difference of the KD values of NSC668036 measured by NMR and fluorescence methods respectively.