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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 1443 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 1205 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 - MAL C12 H22 O11 C([C@@H]1[....
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 (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 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 1NC2 - DOE C27 H41 N5 O10 S c1cc(ccc1C....
7 2HVK - TBA C16 H36 N CCCC[N+](C....
8 5DUB - GLY 5GG GLY ALA n/a n/a
9 5MES ic50 = 0.045 uM 7LT C44 H49 Cl2 N5 O4 CN1CCCN[C@....
10 6FS0 Kd = 0.00017 uM E4W C35 H34 Cl N5 O3 S2 Cc1c-2c(nn....
11 5BJZ - MAL C12 H22 O11 C([C@@H]1[....
12 3PGF - GLC GLC n/a n/a
13 1FE8 - NAG C8 H15 N O6 CC(=O)N[C@....
14 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 1E4X Kd = 25 nM VAL VAL SER HIS PHE ASN ASP n/a n/a
16 4MA7 - P2Z C17 H20 N2 S CN(C)CCCN1....
17 4MA8 - Z80 C17 H19 Cl N2 S CN(C)CCCN1....
18 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
19 4UUJ - XA7 C24 H52 N CCCCCC[N+]....
20 2DWE - TBA C16 H36 N CCCC[N+](C....
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 with APoc: 41
This union binding pocket(no: 1) in the query (biounit: 4dvr.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5HCY 60D 2.28311
2 3EWK FAD 3.30189
3 5CLO NS8 3.38983
4 4GLL NAD 5.11182
5 5LY1 PPI 5.18868
6 4L1F FAD 5.18868
7 3VSV XYS 5.18868
8 1WG8 SAM 5.18868
9 1MFI FHC 5.26316
10 2X52 GYT 5.26316
11 4DC2 ADE 5.66038
12 3ZJX BOG 5.88235
13 3FSY SCA 6.13208
14 5L13 6ZE 6.39269
15 4E93 GUI 6.60377
16 4ZUL UN1 6.84932
17 1Z03 OCH 6.84932
18 3BP1 GUN 7.93103
19 2Z49 AMG 8.01887
20 6C8X BVR 8.08081
21 2XK9 XK9 8.30671
22 2XOC ADP 8.42912
23 4NFE BEN 8.43882
24 4A91 GLU 8.72483
25 3VCA PRO 8.96226
26 4H3Q ANP 8.96226
27 1Y3A GDP 9.26518
28 4DYG MES 9.43396
29 1TMO 2MD 9.90566
30 4URF 1PS 10.0457
31 1F9V ADP 10.3774
32 2NV2 GLN 10.3774
33 2WEL K88 10.6667
34 5CEO 50D 10.8491
35 6F5W KG1 10.9589
36 1O9U ADZ 12.3288
37 2IVF MGD 12.7358
38 3CBC DBS 13.1313
39 1A5Z FBP 14.6226
40 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 15.7895
41 2BVE PH5 28.5714
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