Receptor
PDB id Resolution Class Description Source Keywords
4I53 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CLADE C1086 HIV-1 GP120 CORE IN COMPLEX II-121 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 HIV GP120 ENTRY INHIBITOR DMJ-II-121 CD4-MIMETIC VIRAL INHIBITOR COMPLEX C1086 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG A:503;
B:507;
B:508;
A:502;
B:506;
B:505;
B:503;
A:508;
B:504;
A:504;
A:507;
A:506;
A:505;
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;
submit data
221.208 C8 H15 N O6 CC(=O...
1C1 A:501;
B:501;
Valid;
Valid;
none;
none;
Kd = 110 nM
404.846 C19 H20 Cl F N5 O2 c1ccc...
ASN ILE THR GLY LEU LEU LEU LEU ARG ASP A:448;
B:448;
Invalid;
Invalid;
none;
none;
submit data n/a n/a n/a n/a
FMT B:502;
Invalid;
none;
submit data
46.025 C H2 O2 C(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4I53 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CLADE C1086 HIV-1 GP120 CORE IN COMPLEX II-121 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 HIV GP120 ENTRY INHIBITOR DMJ-II-121 CD4-MIMETIC VIRAL INHIBITOR COMPLEX C1086 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 (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4I53 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 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 4I54 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
4 4DVW - 0M4 C16 H19 Cl F N3 O2 c1cc(c(cc1....
5 4DKP Kd = 1.9 uM 0LL C17 H15 Cl F N3 O2 c1ccc2c(c1....
6 4RZ8 ic50 ~ 270 nM 3ZM C22 H25 Cl N4 O2 S Cc1c(sc(n1....
7 5U6E - 82M C18 H18 Cl F N4 O2 S Cc1c(sc(n1....
8 4DVT - 0LZ C18 H17 Cl F N3 O2 c1ccc2c(c1....
9 4DKR Kd = 0.3 uM 0LJ C18 H17 Cl F N5 O2 [H]/N=C(/N....
10 4DVV - 0M1 C15 H19 Cl F N3 O4 CC1(O[C@H]....
11 4DKO Kd = 0.3 uM 0LM C18 H25 Cl F N3 O2 CC1(CC(CC(....
12 4DVS - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
13 4I53 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 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 4I54 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
4 4DVW - 0M4 C16 H19 Cl F N3 O2 c1cc(c(cc1....
5 4DKP Kd = 1.9 uM 0LL C17 H15 Cl F N3 O2 c1ccc2c(c1....
6 4RZ8 ic50 ~ 270 nM 3ZM C22 H25 Cl N4 O2 S Cc1c(sc(n1....
7 5U6E - 82M C18 H18 Cl F N4 O2 S Cc1c(sc(n1....
8 4DVT - 0LZ C18 H17 Cl F N3 O2 c1ccc2c(c1....
9 4DKR Kd = 0.3 uM 0LJ C18 H17 Cl F N5 O2 [H]/N=C(/N....
10 4DVV - 0M1 C15 H19 Cl F N3 O4 CC1(O[C@H]....
11 4DKO Kd = 0.3 uM 0LM C18 H25 Cl F N3 O2 CC1(CC(CC(....
12 4DVS - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
13 4I53 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 1C1; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 1C1 1 1
2 0LL 0.641975 0.727273
3 0LK 0.609195 0.836364
4 0LJ 0.609195 0.836364
5 0LZ 0.483871 0.655738
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4I53; Ligand: 1C1; Similar sites found: 47
This union binding pocket(no: 1) in the query (biounit: 4i53.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1WAP TRP 0.01052 0.40471 None
2 5LY1 PPI 0.001583 0.47519 1.11732
3 3VCA PRO 0.01174 0.41524 1.39665
4 3SRV S19 0.006426 0.41463 1.44404
5 1RYD GLC 0.009666 0.42786 1.95531
6 1K0E TRP 0.0135 0.4034 1.95531
7 3CBC DBS 0.0003834 0.50238 2.0202
8 3SAO DBH 0.001892 0.45923 2.5
9 1O9U ADZ 0.01144 0.42212 2.57143
10 4M37 SAH 0.004621 0.40638 2.91545
11 4FK7 P34 0.03287 0.40165 3.05677
12 1YFS ALA 0.01005 0.42265 3.07263
13 2F2U M77 0.01261 0.40879 3.35196
14 3JU6 ANP 0.006456 0.43246 3.51351
15 5M8T 0TR 0.02911 0.40081 3.63128
16 3GD9 GLC BGC BGC BGC 0.01582 0.40012 3.63128
17 2QHS OCA 0.0145 0.40583 3.79747
18 1VBJ CIT 0.004087 0.45499 3.91459
19 4WOE ADP 0.01088 0.42305 4.18994
20 2QHV OC9 0.01403 0.4107 4.28571
21 4A91 GLU 0.01806 0.4067 4.36242
22 3EWK FAD 0.003502 0.41504 4.40529
23 4OKD GLC GLC GLC 0.02448 0.40147 4.46927
24 1JPA ANP 0.01452 0.40448 4.48718
25 5TH5 MET 0.02747 0.40159 4.56274
26 2V7O DRN 0.01663 0.40701 4.7619
27 1TIQ COA 0.007745 0.41087 5.58659
28 3UDG TMP 0.03858 0.40571 5.98007
29 1MFI FHC 0.0009804 0.47997 6.14035
30 5EWK P34 0.0239 0.40376 6.5
31 1HQL GLA MBG 0.01142 0.41675 6.61479
32 1HBK COA 0.008629 0.43212 6.74157
33 5KJW 53C 0.02185 0.40476 6.98324
34 2X52 GYT 0.01025 0.41752 7.01754
35 4MOB ADP 0.01928 0.40938 7.22892
36 4AGS GSH 0.01744 0.41031 7.82123
37 1Z0N BCD 0.02374 0.40159 8.33333
38 1SC3 MLI 0.01615 0.4054 8.42697
39 5XVQ 8GC 0.01803 0.40868 8.4507
40 5CLO NS8 0.003015 0.45209 8.47458
41 1TZD ADP 0.01673 0.41732 8.72727
42 4NZ6 DLY 0.01258 0.41948 9.21788
43 3ZZS TRP 0.01066 0.40444 9.23077
44 4GDX GLU 0.0189 0.40837 10.7692
45 1KDK DHT 0.002896 0.40394 12.9944
46 3H9R TAK 0.01572 0.40823 14.6789
47 4DC2 ADE 0.01525 0.41488 17.8571
Pocket No.: 2; Query (leader) PDB : 4I53; Ligand: 1C1; Similar sites found: 13
This union binding pocket(no: 2) in the query (biounit: 4i53.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5F7J ADE 0.01971 0.40593 1.5625
2 2PNC CLU 0.02149 0.40514 1.95531
3 2OG7 AHB 0.02461 0.40144 2.80112
4 3BP1 GUN 0.002121 0.47096 3.10345
5 2FMD MAN MAN 0.01621 0.40378 3.33333
6 4DYG MES 0.01497 0.41746 3.68852
7 2GQS C2R 0.008422 0.40734 3.79747
8 3ZJX BOG 0.02115 0.40397 5.19031
9 4CFU 2WC 0.01412 0.40068 6.27063
10 2Z49 AMG 0.004799 0.43451 8.65922
11 2TOH HBI 0.01941 0.40884 9.0379
12 4Q3F TLA 0.02574 0.40802 11.1111
13 1UNH IXM 0.009773 0.40436 11.9863
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