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Table 2 Clustering results of the ten bound forms

From: Dynamical Basis for Drug Resistance of HIV-1 Protease

PDB id Mutation RMSD (Å) Coupled with the active site Coupled with the flap region
2FNS 7 (substrate) Q7K, D25N, L63P, I64V 0.52 10 23 24 25 26 27 28 29 30 31 84 85 86 87 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83
1HPV 6 (Amprenavir) None 0.54 10 23 24 25 26 27 28 29 30 31 32 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 84
1HXB 6 (Saquinavir) None 0.31 10 23 24 25 26 27 28 29 30 31 32 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 84
1MUI 5 (Lopinavir) N37S 0.53 10 23 24 25 26 27 28 29 30 31 32 84 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83
2O4K 8 (Atazanavir) Q7K 0.35 23 24 25 26 27 28 29 30 31 32 83 84 85 86 87 88 89 90 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 76 77 78 79 80 81 82
3JVY 6 (Darunavir) Q7K, L33I*, L63I, C67A, G86A, C95A 0.38 23 24 25 26 27 28 29 30 31 32 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 79 80 81 82 83 84
2O4P 8 (Tipranavir) Q7K 0.39 23 24 25 26 27 28 29 30 31 32 83 84 85 86 87 88 89 90 44 45 46 47 48 49 50 51 52 53 54 55 56 79 80 81 82 83 84
1HXW 6 (Ritonavir) None 0.40 10 23 24 25 26 27 28 29 30 31 85 86 87 44 45 46 47 48 49 50 51 52 53 54 55 56 79 80 81 82 83 84
2PYN 6 (Nelfinavir) D30N, A71V* 0.26 10 23 24 25 26 27 28 29 30 31 32 84 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83
2B7Z 7 (Indinavir) K20R*, V32I*, L33F*, M36I*, M46I*, L63P, A71V*,V82A*, I84V*, L90M* 0.32 10 22 23 24 25 26 27 28 29 84 85 86 34 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 76 77 78 79 80 81 82 83
  1. The type of the ligand is listed in brackets. The global average RMSD of backbone atoms between the unbound (PDB id 1HHP) and bound forms is given. The mutations of each protease are listed. Only the clusters containing the active site and the flap are shown here.
  2. (1) *drug-resistance mutations
  3. (2) Residues belonging to the 21 common resistant mutations are underlined.
  4. (3) Residues shared by all the bound forms are in italics.