Receptor
PDB id Resolution Class Description Source Keywords
3EBZ 1.2 Å EC: 3.4.23.16 HIGH RESOLUTION HIV-2 PROTEASE STRUCTURE IN COMPLEX WITH CLI DARUNAVIR HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (IROD) HIV-2 ASPARTIC PROTEASE INHIBITORPROTEASE-DRUG COMPLEX H
Ref.: STRUCTURAL EVIDENCE FOR EFFECTIVENESS OF DARUNAVIR 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
017 B:201;
 Valid;
 none;
 submit data
547.664 C27 H37 N3 O7 S CC(C)...
CL A:503;
B:501;
B:502;
B:504;
B:505;
B:506;
B:507;
B:508;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
35.453 Cl [Cl-]
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;
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;
 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: 017; Similar ligands found: 92
No: Ligand ECFP6 Tc MDL keys Tc
1 017 1 1
2 K13 0.877551 0.964706
3 G08 0.876289 0.964286
4 A60 0.867347 0.941176
5 DJR 0.857143 0.941176
6 NJ4 0.838384 0.963855
7 NJM 0.838384 0.952381
8 NJA 0.838384 0.963855
9 G07 0.838384 0.963855
10 BVR 0.83 0.930233
11 NG4 0.813725 0.952381
12 NF7 0.813725 0.952381
13 NFJ 0.745283 0.905882
14 K2A 0.745283 0.918605
15 NE7 0.745283 0.929412
16 NEJ 0.745283 0.929412
17 NF4 0.745283 0.905882
18 F53 0.735849 0.895349
19 NJG 0.733945 0.918605
20 065 0.733945 0.930233
21 NJ7 0.733945 0.918605
22 NJ1 0.724771 0.895349
23 NJJ 0.724771 0.895349
24 52U 0.714286 0.896552
25 G53 0.709402 0.909091
26 QFI 0.706422 0.879121
27 B4R 0.698113 0.876405
28 C7J 0.685185 0.942529
29 478 0.679612 0.963855
30 4UX 0.678899 0.953488
31 G10 0.666667 0.942529
32 P3V 0.663636 0.976471
33 C7L 0.660714 0.976471
34 G43 0.657895 0.879121
35 KGQ 0.655172 0.888889
36 0TQ 0.650406 0.861702
37 G52 0.623932 0.941176
38 5B7 0.608696 0.908046
39 6KK 0.608696 0.918605
40 74T 0.595588 0.88172
41 52W 0.594828 0.918605
42 G04 0.59292 0.918605
43 G79 0.591667 0.918605
44 FQ4 0.582609 0.857143
45 4UY 0.582609 0.91954
46 5B5 0.579832 0.88764
47 53F 0.576271 0.953488
48 G05 0.5625 0.906977
49 FQ1 0.559322 0.857143
50 8FM 0.558333 0.896552
51 6KQ 0.552846 0.873563
52 T1R 0.54918 0.906977
53 Q1D 0.545455 0.876405
54 385 0.544776 0.888889
55 G89 0.542373 0.917647
56 GRL 0.538462 0.928571
57 G55 0.533898 0.873563
58 OQD 0.528926 0.629214
59 OQA 0.528926 0.629214
60 ORV 0.525862 0.625
61 OQG 0.521008 0.636364
62 6KR 0.520325 0.897727
63 OQV 0.516949 0.640449
64 0JV 0.516129 0.906977
65 OQY 0.508475 0.640449
66 52Z 0.508333 0.918605
67 OQ7 0.504065 0.606742
68 HWY 0.504 0.847826
69 OP7 0.5 0.606742
70 J0S 0.495935 0.873563
71 OO4 0.495868 0.606742
72 OR1 0.491935 0.617977
73 OPJ 0.491935 0.622222
74 OQP 0.491935 0.622222
75 7O7 0.464789 0.89011
76 GR6 0.45 0.806452
77 T2R 0.447552 0.909091
78 GR7 0.443662 0.815217
79 GR8 0.432432 0.851064
80 GR5 0.432432 0.851064
81 MUI 0.430769 0.817204
82 M73 0.429752 0.804598
83 MZ9 0.423729 0.761364
84 GA5 0.423358 0.806818
85 M86 0.421875 0.762887
86 MUT 0.414815 0.817204
87 MK5 0.412698 0.76087
88 031 0.411765 0.842697
89 GA8 0.410072 0.8
90 D78 0.408759 0.791667
91 G64 0.40146 0.755319
92 G61 0.4 0.793103
Similar Ligands (3D)
Ligand no: 1; Ligand: 017; Similar ligands found: 11
No: Ligand Similarity coefficient
1 0KJ 0.9220
2 MZ6 0.9192
3 MZ8 0.9160
4 190 0.8903
5 MZ7 0.8671
6 MZ5 0.8617
7 MUV 0.8613
8 MUU 0.8592
9 MZ3 0.8565
10 MZ1 0.8559
11 MZ2 0.8548
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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