Receptor
PDB id Resolution Class Description Source Keywords
4DVR 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF YU2 GP120 CORE IN COMPLEX WITH FAB 48D 557 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GRSUBTYPE B (ISOLATE YU-2) HIV-1 GP120 CD4 BINDING SITE NBD-557 IMMUNE SYSTEM-TRANSCINHIBITOR 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
NAG G:502;
G:505;
G:504;
G:503;
G:501;
G:506;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
0LY G:508;
Valid;
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
4DVR 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF YU2 GP120 CORE IN COMPLEX WITH FAB 48D 557 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GRSUBTYPE B (ISOLATE YU-2) HIV-1 GP120 CD4 BINDING SITE NBD-557 IMMUNE SYSTEM-TRANSCINHIBITOR 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
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 3U7Y - FLC C6 H5 O7 C(C(=O)[O-....
2 3KDM Kd = 0.1 uM TES C19 H28 O2 C[C@]12CC[....
3 5BJZ - GLC GLC n/a n/a
4 3PGF - GLC GLC n/a n/a
5 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
50% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 3U7Y - FLC C6 H5 O7 C(C(=O)[O-....
2 1NC4 - DOF C23 H33 N5 O10 c1cc(ccc1C....
3 6PXH - DHF C19 H21 N7 O6 c1cc(ccc1C....
4 5DS8 - GLY 5CT GLY ALA n/a n/a
5 5DRN - 5CT C10 H23 N3 O3 C(CCNC[C@H....
6 6C5K Kd = 68.5 nM GP1 Z9M KDO KDO KDO n/a n/a
7 3KDM Kd = 0.1 uM TES C19 H28 O2 C[C@]12CC[....
8 1NC2 - DOE C27 H41 N5 O10 S c1cc(ccc1C....
9 2HVK - TBA C16 H36 N CCCC[N+](C....
10 5DUB - GLY 5GG GLY ALA n/a n/a
11 5MES Kd = 0.34 uM 7LT C44 H49 Cl2 N5 O4 CN1CCCN[C@....
12 6FS0 Kd = 0.00017 uM E4W C35 H34 Cl N5 O3 S2 Cc1c-2c(nn....
13 5BJZ - GLC GLC n/a n/a
14 3PGF - GLC GLC n/a n/a
15 1FE8 - NAG C8 H15 N O6 CC(=O)N[C@....
16 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
17 1E4X Kd = 25 nM VAL VAL SER HIS PHE ASN ASP n/a n/a
18 4MA7 - P2Z C17 H20 N2 S CN(C)CCCN1....
19 4MA8 - Z80 C17 H19 Cl N2 S CN(C)CCCN1....
20 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
21 4UUJ - XA7 C24 H52 N CCCCCC[N+]....
22 6NFV - 1EM C26 H50 O5 CCCCCCCCCC....
23 6NFU - 1EM C26 H50 O5 CCCCCCCCCC....
24 2DWE - TBA C16 H36 N CCCC[N+](C....
25 1MJJ Kd = 1.83 nM HAL C23 H29 N2 O7 P c1ccc(cc1)....
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 : 4DVR; Ligand: 0LY; 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: 4dvr.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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