Table 3. Hydrogen bonds formed by CD27 in the minor groove of d(AAAATTTT)2 and external interactions with neighbouring phosphates.
All values are given in Å. A spatial representation of drugs D and E is shown in Figs. 2 ▶(b) and 3 ▶(b). The hydrogen bonds are ordered from the centre to the end of the duplex.
| Atoms involved | Drug D | Drug E | Drug F |
|---|---|---|---|
| N3(A4)–N4(CD27) | 3.06 | 2.88 | 2.77 |
| O2(T6′)–N4(CD27) | 3.08 | 3.24 | 3.26 |
| N3(A2)–N3(CD27) | 3.28 | 3.36 | 3.34 |
| O2(T8′)–N3(CD27) | 2.90 | 3.00 | 2.80 |
| N1(CD27)–OP1(A2 oligo B′) | 3.27 | — | — |
| N7(CD27)–OP2(A3 oligo B′) | 3.14 | — | — |
| N7(CD27)–OP1(A3 oligo B′) | 3.24 | — | — |
| N2(CD27)–OP1(A3 oligo B′) | — | 3.01 | — |