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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.
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BMC Structural Biology

ISSN: 1472-6807

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