Receptor
PDB id Resolution Class Description Source Keywords
3ECG 1.18 Å EC: 3.4.23.16 HIGH RESOLUTION HIV-2 PROTEASE STRUCTURE IN COMPLEX WITH ANTIVIRAL INHIBITOR GRL-98065 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
065 A:201;
 Valid;
 none;
 submit data
576.658 C28 H36 N2 O9 S CC(C)...
CL A:503;
A:507;
A:509;
B:501;
B:502;
B:504;
B:505;
B:506;
B:508;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
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:402;
A:404;
A:406;
A:407;
A:411;
B:401;
B:403;
B:405;
B:408;
B:409;
B:410;
 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;
Part of Protein;
 none;
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: 065; Similar ligands found: 83
No: Ligand ECFP6 Tc MDL keys Tc
1 065 1 1
2 NJ4 0.733945 0.963855
3 G08 0.733945 0.941176
4 NJM 0.733945 0.952381
5 DJR 0.733945 0.964286
6 G07 0.733945 0.963855
7 017 0.733945 0.930233
8 NJA 0.733945 0.963855
9 BVR 0.727273 0.930233
10 385 0.725806 0.954023
11 NF7 0.714286 0.952381
12 NG4 0.714286 0.952381
13 NF4 0.655172 0.905882
14 NFJ 0.655172 0.905882
15 0TQ 0.653543 0.861702
16 A60 0.652174 0.875
17 F53 0.646552 0.895349
18 K13 0.646552 0.897727
19 NEJ 0.641026 0.929412
20 NE7 0.641026 0.929412
21 K2A 0.641026 0.918605
22 B4R 0.640351 0.876405
23 NJ1 0.638655 0.895349
24 NJJ 0.638655 0.895349
25 NJ7 0.633333 0.918605
26 NJG 0.633333 0.918605
27 G53 0.629921 0.909091
28 52U 0.626087 0.918605
29 QFI 0.621849 0.921348
30 74T 0.6 0.842105
31 G43 0.580645 0.921348
32 KGQ 0.579365 0.931818
33 K53 0.542636 0.83871
34 G52 0.539062 0.964286
35 K62 0.526316 0.83871
36 5B7 0.52381 0.930233
37 6KK 0.52381 0.941176
38 P3V 0.52 0.909091
39 K60 0.518519 0.8125
40 FQ4 0.512 0.877778
41 52W 0.511811 0.941176
42 G79 0.51145 0.941176
43 G04 0.508065 0.941176
44 FQ1 0.503937 0.877778
45 4UY 0.5 0.91954
46 G10 0.5 0.877778
47 C7J 0.5 0.877778
48 5B5 0.5 0.88764
49 4UX 0.496063 0.88764
50 ORV 0.495935 0.625
51 Q1D 0.492308 0.876405
52 OQ7 0.488372 0.606742
53 OQV 0.488 0.640449
54 478 0.487603 0.895349
55 C7L 0.484615 0.909091
56 8FM 0.480916 0.918605
57 G05 0.479675 0.929412
58 6KQ 0.477612 0.895349
59 T1R 0.473684 0.929412
60 OP7 0.473282 0.606742
61 GRL 0.472441 0.928571
62 OO4 0.46875 0.606742
63 OQG 0.46875 0.636364
64 G55 0.46875 0.917647
65 OQY 0.468254 0.640449
66 OQP 0.465649 0.604396
67 OQA 0.465649 0.629214
68 OQD 0.465649 0.629214
69 G89 0.465116 0.940476
70 7O7 0.462585 0.849462
71 GR6 0.458333 0.846154
72 T2R 0.455782 0.866667
73 OR1 0.454545 0.655172
74 OPJ 0.454545 0.604396
75 6KR 0.447761 0.91954
76 0JV 0.444444 0.906977
77 HWY 0.444444 0.827957
78 52Z 0.435115 0.941176
79 GR7 0.432432 0.855556
80 J0S 0.425373 0.895349
81 GR8 0.422078 0.8125
82 GR5 0.422078 0.8125
83 53F 0.419118 0.909091
Similar Ligands (3D)
Ligand no: 1; Ligand: 065; Similar ligands found: 19
No: Ligand Similarity coefficient
1 MZ8 0.9424
2 0KJ 0.9394
3 MZ6 0.9360
4 031 0.9125
5 M73 0.9114
6 MK5 0.8904
7 MZ7 0.8858
8 NKA 0.8852
9 MJD 0.8796
10 JDY 0.8769
11 MUU 0.8759
12 NJY 0.8750
13 M86 0.8705
14 JDV 0.8700
15 MZ5 0.8685
16 MZ3 0.8643
17 190 0.8636
18 MZ2 0.8586
19 MZ9 0.8584
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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