Receptor
PDB id Resolution Class Description Source Keywords
4dkq 1.89 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CLADE A/E 93TH057 HIV-1 GP120 CORE IN C WITH DMJ-I-228 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 HIV-1 GP120 CLADE A/E CD4 MIMIC DMJ-I-228 VIRAL PROTEIN-COMPLEX
Ref.: STRUCTURE-BASED DESIGN, SYNTHESIS, AND CHARACTERIZA DUAL HOTSPOT SMALL-MOLECULE HIV-1 ENTRY INHIBITORS. J.MED.CHEM. V. 55 4382 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0LK A:613;
 Valid;
 none;
 Kd = 0.25 uM
389.811 C18 H17 Cl F N5 O2 [H]/N...
EPE A:612;
 Invalid;
 none;
 submit data
238.305 C8 H18 N2 O4 S C1CN(...
NAG A:601;
A:602;
A:603;
A:604;
A:605;
A:606;
A:607;
A:608;
A:609;
A:610;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
221.208 C8 H15 N O6 CC(=O...
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: 0LK; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 0LK 1 1
2 0LJ 1 1
3 0LL 0.658228 0.875
4 1C1 0.609195 0.836364
5 0LZ 0.462366 0.655172
Similar Ligands (3D)
Ligand no: 1; Ligand: 0LK; Similar ligands found: 0
No: Ligand Similarity coefficient
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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