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 1256 families.
1 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 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 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
5 3PGF - GLC GLC n/a n/a
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 3U7Y - FLC C6 H5 O7 C(C(=O)[O-....
2 1NC4 - DOF C23 H33 N5 O10 c1cc(ccc1C....
3 5DS8 - GLY 5CT GLY ALA n/a n/a
4 5DRN - 5CT C10 H23 N3 O3 C(CCNC[C@H....
5 3KDM Kd = 0.1 uM TES C19 H28 O2 C[C@]12CC[....
6 1QKZ - ALA ASN GLY GLY ALA SER GLY GLN VAL LYS n/a n/a
7 1NC2 - DOE C27 H41 N5 O10 S c1cc(ccc1C....
8 2HVK - TBA C16 H36 N CCCC[N+](C....
9 5DUB - GLY 5GG GLY ALA n/a n/a
10 5MES ic50 = 0.045 uM 7LT C44 H49 Cl2 N5 O4 CN1CCCN[C@....
11 1FE8 - NAG C8 H15 N O6 CC(=O)N[C@....
12 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
13 5T85 - 44G C18 H35 O10 P CCCCCC(=O)....
14 1E4X Kd = 25 nM VAL VAL SER HIS PHE ASN ASP n/a n/a
15 4MA7 - P2Z C17 H20 N2 S CN(C)CCCN1....
16 4MA8 - Z80 C17 H19 Cl N2 S CN(C)CCCN1....
17 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
18 4UUJ - XA7 C24 H52 N CCCCCC[N+]....
19 2DWE - TBA C16 H36 N CCCC[N+](C....
20 3PGF - GLC GLC n/a n/a
21 1MJJ Kd = 1.83 nM HAL C23 H29 N2 O7 P c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 0LY; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 0LY 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DVR; Ligand: 0LY; Similar sites found: 14
This union binding pocket(no: 1) in the query (biounit: 4dvr.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3EWK FAD 0.008795 0.4104 3.30189
2 5CLO NS8 0.01835 0.40084 3.38983
3 3VSV XYS 0.01301 0.40723 5.18868
4 1WG8 SAM 0.01718 0.40473 5.18868
5 2X52 GYT 0.007214 0.41482 5.26316
6 3ZJX BOG 0.01069 0.4137 5.88235
7 1Z03 OCH 0.01774 0.4002 6.84932
8 3BP1 GUN 0.001099 0.47714 7.93103
9 2Z49 AMG 0.004639 0.4252 8.01887
10 2XK9 XK9 0.02066 0.41194 8.30671
11 4A91 GLU 0.008348 0.42201 8.72483
12 4H3Q ANP 0.01756 0.40124 8.96226
13 2IVF MGD 0.01937 0.41741 12.7358
14 2BVE PH5 0.02108 0.40053 28.5714
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