Receptor
PDB id Resolution Class Description Source Keywords
4DVS 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CLADE A/E 93TH057 HIV-1 GP120 CORE IN C WITH NBD-557 HUMAN IMMUNODEFICIENCY VIRUS 1 HIV-1 GP120 SMALL MOLECULE INHIBITOR CD4 BINDING SITE NBDVIRAL PROTEIN-TRANSCRIPTION INHIBITOR COMPLEX
Ref.: CRYSTAL STRUCTURES OF HIV-1 GP120 ENVELOPE GLYCOPRO COMPLEX WITH NBD ANALOGUES THAT TARGET THE CD4-BIND PLOS ONE V. 9 85940 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EPE B:513;
A:513;
Invalid;
Invalid;
none;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
NAG A:503;
B:507;
B:508;
A:509;
A:502;
B:510;
B:502;
B:506;
B:505;
B:503;
A:508;
B:509;
A:510;
B:501;
B:504;
A:504;
A:507;
A:506;
A:505;
A:501;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
0LY B:512;
A:512;
Valid;
Valid;
none;
none;
submit data
382.295 C17 H24 Br N3 O2 CC1(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4I54 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CLADE A/E 93TH057 HIV-1 GP120 H375S COR COMPLEX WITH DMJ-II-121 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 HIV GP120 ENTRY INHIBITOR STRUCTURE-BASED DRUG DESIGN THERMODYNAMICS VIRAL INHIBITION DMJ-II-121 CD4-MIMETIC PROTEIN-INHIBITOR COMPLEX CLADE A/E CD4 EXTRACELLULAR
Ref.: STRUCTURE-BASED DESIGN AND SYNTHESIS OF AN HIV-1 EN INHIBITOR EXPLOITING X-RAY AND THERMODYNAMIC CHARACTERIZATION. ACS MED CHEM LETT V. 4 338 2013
Members (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4DKQ Kd = 0.25 uM 0LK C18 H17 Cl F N5 O2 [H]/N=C(N)....
2 4DVX - 0M5 C16 H19 Cl F N3 O2 c1cc(c(cc1....
3 6ONE - MVY C14 H16 Cl F N2 O3 COC(=O)N1C....
4 6OOO - MXJ C16 H22 Cl F N4 O2 CCCNC(=O)N....
5 4I54 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
6 4DVW - 0M4 C16 H19 Cl F N3 O2 c1cc(c(cc1....
7 6ONH - MWD C16 H21 Cl F N3 O2 CCCNC(=O)N....
8 4DKP Kd = 1.9 uM 0LL C17 H15 Cl F N3 O2 c1ccc2c(c1....
9 6USW - O51 C15 H20 Cl F N4 O2 c1cc(c(cc1....
10 4RZ8 ic50 ~ 270 nM 3ZM C22 H25 Cl N4 O2 S Cc1c(sc(n1....
11 5U6E - 82M C18 H18 Cl F N4 O2 S Cc1c(sc(n1....
12 6ONF - MW4 C15 H18 Cl F N2 O3 CCOC(=O)N1....
13 4DVT - 0LZ C18 H17 Cl F N3 O2 c1ccc2c(c1....
14 4DKR Kd = 0.3 uM 0LJ C18 H17 Cl F N5 O2 [H]/N=C(/N....
15 4DVV - 0M1 C15 H19 Cl F N3 O4 CC1(O[C@H]....
16 4DKO Kd = 0.3 uM 0LM C18 H25 Cl F N3 O2 CC1(CC(CC(....
17 4DVS - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
70% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 4DKQ Kd = 0.25 uM 0LK C18 H17 Cl F N5 O2 [H]/N=C(N)....
2 4DVX - 0M5 C16 H19 Cl F N3 O2 c1cc(c(cc1....
3 6ONE - MVY C14 H16 Cl F N2 O3 COC(=O)N1C....
4 6OOO - MXJ C16 H22 Cl F N4 O2 CCCNC(=O)N....
5 4I54 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
6 4DVW - 0M4 C16 H19 Cl F N3 O2 c1cc(c(cc1....
7 6ONH - MWD C16 H21 Cl F N3 O2 CCCNC(=O)N....
8 4DKP Kd = 1.9 uM 0LL C17 H15 Cl F N3 O2 c1ccc2c(c1....
9 6USW - O51 C15 H20 Cl F N4 O2 c1cc(c(cc1....
10 4RZ8 ic50 ~ 270 nM 3ZM C22 H25 Cl N4 O2 S Cc1c(sc(n1....
11 5U6E - 82M C18 H18 Cl F N4 O2 S Cc1c(sc(n1....
12 6ONF - MW4 C15 H18 Cl F N2 O3 CCOC(=O)N1....
13 4DVT - 0LZ C18 H17 Cl F N3 O2 c1ccc2c(c1....
14 4DKR Kd = 0.3 uM 0LJ C18 H17 Cl F N5 O2 [H]/N=C(/N....
15 4DVV - 0M1 C15 H19 Cl F N3 O4 CC1(O[C@H]....
16 4DKO Kd = 0.3 uM 0LM C18 H25 Cl F N3 O2 CC1(CC(CC(....
17 4DVS - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
18 4I53 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
50% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 4DKQ Kd = 0.25 uM 0LK C18 H17 Cl F N5 O2 [H]/N=C(N)....
2 4DVX - 0M5 C16 H19 Cl F N3 O2 c1cc(c(cc1....
3 6ONE - MVY C14 H16 Cl F N2 O3 COC(=O)N1C....
4 6OOO - MXJ C16 H22 Cl F N4 O2 CCCNC(=O)N....
5 4I54 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
6 4DVW - 0M4 C16 H19 Cl F N3 O2 c1cc(c(cc1....
7 6ONH - MWD C16 H21 Cl F N3 O2 CCCNC(=O)N....
8 4DKP Kd = 1.9 uM 0LL C17 H15 Cl F N3 O2 c1ccc2c(c1....
9 6USW - O51 C15 H20 Cl F N4 O2 c1cc(c(cc1....
10 4RZ8 ic50 ~ 270 nM 3ZM C22 H25 Cl N4 O2 S Cc1c(sc(n1....
11 5U6E - 82M C18 H18 Cl F N4 O2 S Cc1c(sc(n1....
12 6ONF - MW4 C15 H18 Cl F N2 O3 CCOC(=O)N1....
13 4DVT - 0LZ C18 H17 Cl F N3 O2 c1ccc2c(c1....
14 4DKR Kd = 0.3 uM 0LJ C18 H17 Cl F N5 O2 [H]/N=C(/N....
15 4DVV - 0M1 C15 H19 Cl F N3 O4 CC1(O[C@H]....
16 4DKO Kd = 0.3 uM 0LM C18 H25 Cl F N3 O2 CC1(CC(CC(....
17 4DVS - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
18 4I53 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 0LY; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 0LY 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 0LY; Similar ligands found: 17
No: Ligand Similarity coefficient
1 0LM 0.9191
2 BCE 0.8966
3 0M4 0.8937
4 FZ8 0.8857
5 NNF 0.8780
6 CGG 0.8780
7 8XY 0.8769
8 077 0.8742
9 7GK 0.8681
10 B1K 0.8676
11 GYZ 0.8652
12 KV5 0.8590
13 0M1 0.8586
14 KVE 0.8580
15 26Y 0.8556
16 6NE 0.8524
17 OA5 0.8522
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4I54; Ligand: 1C1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4i54.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4I54; Ligand: 1C1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4i54.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
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