Table 3 |
||||
| Contacts observed between inhibitor 2 and N9 NA; 3LV is the residue name assigned to the inhibitor by the PDB and 488 is the residue number of the inhibitor | ||||
| Inhibitor atom | N9 atom | distance (Å) | Angle(D-A-AA)° | |
| Potential hydrogen bonds1 | ||||
| 3LV488-O1 | Arg118-NH1 | 2.84 | 117.3 | |
| 3LV488-O1 | Arg371-NH1 | 2.86 | 112.8 | |
| 3LV488-O2 | Arg292-NH1 | 3.34 | 97.1 | |
| 3LV488-O2 | Arg292-NH2 | 3.25 | 101.2 | |
| 3LV488-O2 | Arg371-NH2 | 2.84 | 124.9 | |
| 3LV488-O2 | HOH-747 | 2.85 | ||
| HOH-747 | 3.25 | Asn347 OD1 | ||
| 3LV488-O15 | Arg152- NH1 | 2.54 | 145.9 | |
| 3LV488-O20 | HOH-612 | 2.72 | ||
| HOH-612 | 2.82, 3.16 | Glu227 OE2, Thr225 O | ||
| Van der Waals contacts2 (≤4.0 Å) | ||||
| 3LV488-C1 | Tyr406-OH | 2.97 | 119.4 | |
| Arg371-NH1 | 3.70 | 96.2 | ||
| Arg371-NH2 | 3.49 | 106.5 | ||
| Tyr406-CZ | 3.83 | 42.5 | ||
| 3LV488-O1 | Tyr406-OH | 3.50 | 99.8 | |
| Arg118-CZ | 3.65 | 43.7 | ||
| Arg118-NH2 | 3.56 | 83.0 | ||
| Arg371-CZ | 3.59 | 47.2 | ||
| Arg371-NH2 | 3.45 | 85.5 | ||
| 3LV488-C2 | Tyr406-OH | 2.80 | 136.4 | |
| 3LV488-O2 | Tyr406-OH | 3.32 | 123.93 | |
| Arg371-CZ | 3.76 | 38.3 | ||
| Arg371-NH1 | 3.82 | 96.2 | ||
| 3LV488-C3 | Tyr406-OH | 3.19 | 161.8 | |
| 3LV488-C6 | Glu119-OE2 | 3.39 | 119.6 | |
| Asp151-CG | 3.49 | 74.6 | ||
| Asp151-OD1 | 3.37 | 84.4 | ||
| Asp151-OD2 | 3.87 | 62.7 | ||
| 3LV488-C7 | Glu119-OE2 | 3.49 | 136.6 | |
| Asp151-OD1 | 3.52 | 97.7 | ||
| Asp151-CG | 3.89 | 63.8 | ||
| Tyr406-OH | 3.23 | 118.0 | ||
| Arg118-NH1 | 3.63 | 113.4 | ||
| 3LV488-C10 | Ile222-CD1 | 3.63 | 122.8 | |
| 3LV488-C11 | Ala246-CB | 3.90 | 115.5 | |
| Ile222-CD1 | 3.54 | 105.5 | ||
| Ile222-CB | 3.88 | 87.6 | ||
| Arg224-CZ | 3.43 | 79.4 | ||
| Arg224-NE | 3.78 | 64.8 | ||
| Arg224-NH1 | 3.44 | 78.4 | ||
| Arg224-NH2 | 3.81 | 63.4 | ||
| HOH-945 | 2.82 | --- | ||
| 3LV488-C14 | Arg292-NH24 | 3.50 | 140.0 | |
| 3LV488-O15 | Asp151-CB | 3.59 | 100.5 | |
| Arg152-CG | 3.84 | 73.6 | ||
| Arg152-CD | 3.71 | 83.0 | ||
| Arg152-CZ | 3.70 | 22.6 | ||
| 3LV488-C16 | Trp178-CE3 | 3.59 | 91.2 | |
| Trp178-CZ3 | 3.88 | 67.8 | ||
| Trp178-O | 3.78 | 135.7 | ||
| Arg152-CD | 3.73 | 78.1 | ||
| Arg152-CG | 3.73 | 78.1 | ||
| 3LV488-C17 | Trp178-O | 3.43 | 139.6 | |
| Glu227-OE2 | 3.62 | 135.8 | ||
| 3LV488-C19 | Trp178-O | 3.19 | 167.7 | |
| Glu119-CD | 3.88 | 85.8 | ||
| 3LV488-O19 | Asp151-O | 3.26 | 116.7 | |
| Asp151-CB | 3.73 | 97.2 | ||
| Arg156-NH1 | 3.68 | 139.0 | ||
| Trp178-O | 2.82 | 162.5 | ||
| 3LV488-C20 | Glu227-CG | 3.88 | 74.3 | |
| Glu227-CD | 3.77 | 55.7 | ||
| Glu227-OE2 | 3.23 | 105.4 | ||
| Glu277-OE2 | 3.34 | 140.2 | ||
| 3LV488-O20 | Glu227-OE2 | 3.68 | 115.2 | |
| Glu277-CG | 3.80 | 70.4 | ||
| Glu277-CD | 3.59 | 31.9 | ||
| Glu277-OE2 | 2.61 | 133.4 | ||
| Water bridge – inhibitor – Glu276 | ||||
| 3LV488-O20 | HOH-612 | 2.72 | ||
| 612-HOH | 553-HOH | 2.64 | ||
| 553-HOH | Glu276-OE1 | 2.82 | 142.2 | |
| Glu276 interactions | ||||
| Glu276-OE1 | Arg224-NE | 2.72 | 114.2 | |
| Glu276-OE2 | Arg224-NE | 3.50 | 83.2 | |
| Glu276-OE2 | Arg224-NH2 | 2.81 | 115.9 | |
| Glu276-OE2 | His274-NE2 | 2.73 | 119.7 | |
1Potential hydrogen bonds were identified using HBPLUS[29]. Potential hydrogen bonds were interactions between donor and acceptor atoms that met the following geometric requirements: (i) a donor acceptor distance (D-A) < 3.5 Å and a hydrogen acceptor distance (H-A) < 2.5 Å and (ii) a donor-acceptor-acceptor antecedent angle (D-A-AA), of > 90° [31].
2Favorable hydrophobic contacts were defined as non-bonded contacts between two carbon atoms at a distance of ≤4 Å [28].
3Freely rotating hydroxyl hydrogen atoms had the potential to form hydrogen bonds with two alternative acceptor atoms. Only the more probable acceptor atom at the shorter distance from the hydrogen atom was reported by HBPLUS.
4There were several conformations of the propyl chain C12-C14. We used the best, but it is of low occupancy so the interactions involving C14 contribute very little.
Venkatramani et al. BMC Structural Biology 2012 12:7 doi:10.1186/1472-6807-12-7
