Receptor
PDB id Resolution Class Description Source Keywords
3EC0 1.18 Å EC: 3.4.23.16 HIGH RESOLUTION HIV-2 PROTEASE STRUCTURE IN COMPLEX WITH ANTIVIRAL INHIBITOR GRL-06579A HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE ROD) HIV-2 ASPARTIC PROTEASE INHIBITOR PROTEASE-INHIBITOR COMPLEX HYDROLASE
Ref.: STRUCTURAL EVIDENCE FOR EFFECTIVENESS OF DARUNAVIR AND TWO RELATED ANTIVIRAL INHIBITORS AGAINST HIV-2 PROTEASE J.MOL.BIOL. V. 384 178 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:507;
A:508;
B:501;
B:502;
B:503;
B:504;
B:505;
B:506;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
35.453 Cl [Cl-]
GRL A:201;
 Valid;
 none;
 submit data
560.702 C29 H40 N2 O7 S CC(C)...
IMD A:304;
A:306;
B:301;
B:302;
B:303;
B:305;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
69.085 C3 H5 N2 c1c[n...
NA A:601;
 Part of Protein;
 none;
 submit data
22.99 Na [Na+]
ZN A:403;
A:405;
A:406;
A:410;
B:401;
B:402;
B:404;
B:407;
B:408;
B:409;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1IDA 1.7 Å EC: 3.4.23.16 CRYSTAL STRUCTURES OF HIV-2 PROTEASE IN COMPLEX WITH INHIBIT CONTAINING THE HYDROXYETHYLAMINE DIPEPTIDE ISOSTERE HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 ACID PROTEINASE AIDS PROTEASE HYDROLASE-HYDROLASE INHIBITCOMPLEX
Ref.: CRYSTAL STRUCTURES OF HIV-2 PROTEASE IN COMPLEX WIT INHIBITORS CONTAINING THE HYDROXYETHYLAMINE DIPEPTI ISOSTERE. STRUCTURE V. 3 33 1995
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 1JLD ic50 = 185 nM 0PP C37 H51 N5 O6 CCC(CC)NC(....
2 3EBZ - 017 C27 H37 N3 O7 S CC(C)C[N@@....
3 3ECG - 065 C28 H36 N2 O9 S CC(C)C[N@@....
4 5UPJ Ki = 75 nM UIN C20 H24 O3 CC[C@@H](c....
5 6UPJ Ki = 480 nM NIU C19 H22 O3 CC[C@@H](c....
6 4UPJ Ki = 0.16 uM U04 C25 H28 N2 O6 CC[C@@H](c....
7 1HSH Ki = 2.45 nM MK1 C36 H47 N5 O4 CC(C)(C)NC....
8 3S45 Ki = 3.24 nM 478 C25 H35 N3 O6 S CC(C)C[N@]....
9 3UPJ Ki = 0.56 uM U03 C19 H18 O4 CCC(c1cccc....
10 2MIP ic50 < 3.5 nM PHE VAL PHE LEU GLU ILE NH2 n/a n/a
11 1IVP Ki = 30 nM 1ZK C45 H62 N7 O7 CC[C@H](C)....
12 3EC0 - GRL C29 H40 N2 O7 S CC(C)CN(C[....
13 1IDB ic50 = 11 nM 0DO C35 H46 N4 O6 S Cc1cccc(c1....
14 1IDA ic50 < 2 nM 0PO C41 H52 N6 O4 S CC(C)[C@@H....
15 1HII Ki = 53 nM C20 C31 H51 N5 O5 CC(C)[C@@H....
70% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 1JLD ic50 = 185 nM 0PP C37 H51 N5 O6 CCC(CC)NC(....
2 3EBZ - 017 C27 H37 N3 O7 S CC(C)C[N@@....
3 3ECG - 065 C28 H36 N2 O9 S CC(C)C[N@@....
4 5UPJ Ki = 75 nM UIN C20 H24 O3 CC[C@@H](c....
5 6UPJ Ki = 480 nM NIU C19 H22 O3 CC[C@@H](c....
6 4UPJ Ki = 0.16 uM U04 C25 H28 N2 O6 CC[C@@H](c....
7 1HSH Ki = 2.45 nM MK1 C36 H47 N5 O4 CC(C)(C)NC....
8 3S45 Ki = 3.24 nM 478 C25 H35 N3 O6 S CC(C)C[N@]....
9 3UPJ Ki = 0.56 uM U03 C19 H18 O4 CCC(c1cccc....
10 2MIP ic50 < 3.5 nM PHE VAL PHE LEU GLU ILE NH2 n/a n/a
11 1IVP Ki = 30 nM 1ZK C45 H62 N7 O7 CC[C@H](C)....
12 3EC0 - GRL C29 H40 N2 O7 S CC(C)CN(C[....
13 1IDB ic50 = 11 nM 0DO C35 H46 N4 O6 S Cc1cccc(c1....
14 1IDA ic50 < 2 nM 0PO C41 H52 N6 O4 S CC(C)[C@@H....
15 1HII Ki = 53 nM C20 C31 H51 N5 O5 CC(C)[C@@H....
16 1TCW Ki = 960 nM IM1 C31 H42 N4 O4 CC(C)[C@@H....
17 1YTI - PHE LEU GLU LYS n/a n/a
18 1SIV Ki = 8.4 nM PSI C29 H47 N5 O7 C[C@@H](C(....
19 1YTJ - PPN GLU ALA NLE SER n/a n/a
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 1JLD ic50 = 185 nM 0PP C37 H51 N5 O6 CCC(CC)NC(....
2 3EBZ - 017 C27 H37 N3 O7 S CC(C)C[N@@....
3 3ECG - 065 C28 H36 N2 O9 S CC(C)C[N@@....
4 5UPJ Ki = 75 nM UIN C20 H24 O3 CC[C@@H](c....
5 6UPJ Ki = 480 nM NIU C19 H22 O3 CC[C@@H](c....
6 4UPJ Ki = 0.16 uM U04 C25 H28 N2 O6 CC[C@@H](c....
7 1HSH Ki = 2.45 nM MK1 C36 H47 N5 O4 CC(C)(C)NC....
8 3S45 Ki = 3.24 nM 478 C25 H35 N3 O6 S CC(C)C[N@]....
9 3UPJ Ki = 0.56 uM U03 C19 H18 O4 CCC(c1cccc....
10 2MIP ic50 < 3.5 nM PHE VAL PHE LEU GLU ILE NH2 n/a n/a
11 1IVP Ki = 30 nM 1ZK C45 H62 N7 O7 CC[C@H](C)....
12 3EC0 - GRL C29 H40 N2 O7 S CC(C)CN(C[....
13 1IDB ic50 = 11 nM 0DO C35 H46 N4 O6 S Cc1cccc(c1....
14 1IDA ic50 < 2 nM 0PO C41 H52 N6 O4 S CC(C)[C@@H....
15 1HII Ki = 53 nM C20 C31 H51 N5 O5 CC(C)[C@@H....
16 1TCW Ki = 960 nM IM1 C31 H42 N4 O4 CC(C)[C@@H....
17 1YTI - PHE LEU GLU LYS n/a n/a
18 1SIV Ki = 8.4 nM PSI C29 H47 N5 O7 C[C@@H](C(....
19 1YTJ - PPN GLU ALA NLE SER n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GRL; Similar ligands found: 71
No: Ligand ECFP6 Tc MDL keys Tc
1 GRL 1 1
2 G05 0.679612 0.904762
3 NJM 0.651376 0.975309
4 031 0.623932 0.860465
5 G89 0.621622 0.939024
6 478 0.613208 0.915663
7 0JV 0.603448 0.927711
8 HWY 0.603448 0.824176
9 G55 0.598214 0.870588
10 J0S 0.596491 0.892857
11 F53 0.568965 0.915663
12 K2A 0.564103 0.939759
13 5B5 0.563025 0.906977
14 52U 0.561404 0.916667
15 DJR 0.551724 0.939759
16 5B7 0.550847 0.905882
17 52W 0.550847 0.916667
18 G04 0.547826 0.916667
19 B4R 0.547826 0.895349
20 BVR 0.547009 0.928571
21 8FM 0.541667 0.916667
22 NJA 0.538462 0.962963
23 4UY 0.538462 0.895349
24 017 0.538462 0.928571
25 G08 0.538462 0.939759
26 G07 0.538462 0.962963
27 NJ4 0.538462 0.962963
28 NF7 0.537815 0.975309
29 NG4 0.537815 0.975309
30 G79 0.536585 0.939759
31 T1R 0.532787 0.904762
32 Q1D 0.528926 0.895349
33 4UX 0.521008 0.885057
34 G52 0.516129 0.939759
35 C7J 0.512605 0.875
36 C7L 0.508197 0.906977
37 G10 0.5 0.875
38 G53 0.488722 0.906977
39 52Z 0.479339 0.916667
40 NJJ 0.47619 0.915663
41 NJ1 0.47619 0.915663
42 NFJ 0.475806 0.903614
43 NF4 0.475806 0.903614
44 NJG 0.472441 0.939759
45 065 0.472441 0.928571
46 NJ7 0.472441 0.939759
47 A60 0.471545 0.872093
48 K13 0.467742 0.895349
49 NE7 0.464 0.927711
50 NEJ 0.464 0.927711
51 FQ4 0.463415 0.875
52 QFI 0.460317 0.876405
53 53F 0.460317 0.885057
54 8HD 0.453846 0.813953
55 MUI 0.448819 0.774194
56 M73 0.436975 0.843373
57 FQ1 0.433071 0.875
58 MUT 0.431818 0.774194
59 MZ9 0.431034 0.797619
60 7O7 0.430556 0.866667
61 KGQ 0.428571 0.886364
62 G43 0.427481 0.876405
63 0TQ 0.425532 0.83871
64 T2R 0.423611 0.863636
65 MK5 0.419355 0.816092
66 GA5 0.419118 0.823529
67 M86 0.417323 0.795699
68 GA8 0.416058 0.816092
69 D78 0.414815 0.75
70 G61 0.406504 0.831325
71 74T 0.405229 0.83871
Similar Ligands (3D)
Ligand no: 1; Ligand: GRL; Similar ligands found: 8
No: Ligand Similarity coefficient
1 P3V 0.9333
2 0KJ 0.9272
3 MZ8 0.8877
4 6KK 0.8844
5 MZ6 0.8803
6 6KR 0.8778
7 MZ1 0.8569
8 MZ7 0.8522
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1IDA; Ligand: 0PO; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 1ida.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 3WSJ MK1 30.303
2 3WSJ MK1 30.303
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