Receptor
PDB id Resolution Class Description Source Keywords
2ymd 1.96 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF A MUTANT BINDING PROTEIN (5HTBP-ACHBP) IN COMPLEX WITH SEROTONIN (5-HYDROXYTRYPTAMINE) APLYSIA CALIFORNICA RECEPTOR PENTAMERIC LIGAND-GATED ION CHANNEL
Ref.: STRUCTURAL BASIS OF LIGAND RECOGNITION IN 5-HT(3) R EMBO REP. V. 14 49 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1214;
B:1211;
B:1213;
B:1215;
C:1214;
D:1213;
D:1215;
D:1216;
E:1214;
F:1213;
F:1215;
F:1217;
G:1215;
J:1215;
Invalid;
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;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PO4 A:1215;
B:1214;
C:1215;
D:1217;
E:1215;
F:1216;
G:1214;
H:1207;
I:1214;
J:1214;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
SRO A:1213;
B:1212;
C:1213;
D:1214;
E:1213;
F:1214;
G:1213;
H:1206;
I:1213;
J:1213;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
Kd = 693 uM
176.215 C10 H12 N2 O c1cc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2BYS 2.05 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF ACHBP FROM APLYSIA CALIFORNICA IN COMPLEX WITH LOBELINE APLYSIA CALIFORNICA ACETYLCHOLINE BINDING PROTEIN NICOTINIC ACETYLCHOLINE CONFORMATIONAL FLEXIBILITY LOBELINE RECEPTOR
Ref.: STRUCTURES OF APLYSIA ACHBP COMPLEXES WITH NICOTINIC AGONISTS AND ANTAGONISTS REVEAL DISTINCTIVE BINDING INTERFACES AND CONFORMATIONS. EMBO J. V. 24 3635 2005
Members (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 263 families.
1 2WNC Kd = 479 nM TKT C17 H20 N2 O2 CN1[C@H]2C....
2 2XYT Ki = 509.2 nM TC9 C37 H42 N2 O6 C[N@H+]1CC....
3 2YMD Kd = 693 uM SRO C10 H12 N2 O c1cc2c(cc1....
4 4DBM Kd = 24 nM 0J0 C22 H28 N5 O2 CN1c2ccccc....
5 3C79 Kd = 63 nM IM4 C9 H10 Cl N5 O2 c1cc(ncc1C....
6 2BYR Kd = 2.8 nM MLK C37 H50 N2 O10 CC[N@]1C[C....
7 4XHE - 40P C41 H61 N O9 C[C@H]1C[C....
8 2WNJ Kd = 330 nM ZY7 C19 H20 N2 O2 COc1ccc(c(....
9 2BYS Kd = 0.3 nM LOB C22 H27 N O2 C[N@@]1[C@....
10 2PGZ Kd = 1.8 uM COC C17 H21 N O4 C[N@]1[C@H....
11 2XNV Ki = 5 uM VU3 C21 H24 N2 c1ccc(cc1)....
12 5AIN - QMR C13 H13 N3 c1cnc2cc3c....
13 2WN9 Kd = 3 nM ZY5 C18 H18 N2 O2 COc1cc(ccc....
14 3C84 Kd = 14 nM TH4 C10 H9 Cl N4 S c1cc(ncc1C....
15 2XYS Ki = 38 nM SY9 C21 H22 N2 O2 c1ccc2c(c1....
16 4BFQ - 083 C21 H18 N6 Cc1cc(nc(n....
17 4XK9 - 41J C42 H63 N O7 C[C@H]1C[C....
18 2YME Kd = 549 nM CWB C18 H24 N4 O Cn1c2ccccc....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 196 families.
1 2WNC Kd = 479 nM TKT C17 H20 N2 O2 CN1[C@H]2C....
2 2XYT Ki = 509.2 nM TC9 C37 H42 N2 O6 C[N@H+]1CC....
3 2YMD Kd = 693 uM SRO C10 H12 N2 O c1cc2c(cc1....
4 4DBM Kd = 24 nM 0J0 C22 H28 N5 O2 CN1c2ccccc....
5 3C79 Kd = 63 nM IM4 C9 H10 Cl N5 O2 c1cc(ncc1C....
6 2BYR Kd = 2.8 nM MLK C37 H50 N2 O10 CC[N@]1C[C....
7 4XHE - 40P C41 H61 N O9 C[C@H]1C[C....
8 2WNJ Kd = 330 nM ZY7 C19 H20 N2 O2 COc1ccc(c(....
9 2BYS Kd = 0.3 nM LOB C22 H27 N O2 C[N@@]1[C@....
10 2PGZ Kd = 1.8 uM COC C17 H21 N O4 C[N@]1[C@H....
11 2XNV Ki = 5 uM VU3 C21 H24 N2 c1ccc(cc1)....
12 5AIN - QMR C13 H13 N3 c1cnc2cc3c....
13 2WN9 Kd = 3 nM ZY5 C18 H18 N2 O2 COc1cc(ccc....
14 3C84 Kd = 14 nM TH4 C10 H9 Cl N4 S c1cc(ncc1C....
15 2XYS Ki = 38 nM SY9 C21 H22 N2 O2 c1ccc2c(c1....
16 4BFQ - 083 C21 H18 N6 Cc1cc(nc(n....
17 4XK9 - 41J C42 H63 N O7 C[C@H]1C[C....
18 2YME Kd = 549 nM CWB C18 H24 N4 O Cn1c2ccccc....
19 5LXB - 7A9 C19 H24 N2 O c1cc2c3c(c....
20 4ZJS - 4P0 C10 H15 N O CC(=O)C1=C....
50% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 171 families.
1 2WNC Kd = 479 nM TKT C17 H20 N2 O2 CN1[C@H]2C....
2 2XYT Ki = 509.2 nM TC9 C37 H42 N2 O6 C[N@H+]1CC....
3 2YMD Kd = 693 uM SRO C10 H12 N2 O c1cc2c(cc1....
4 4DBM Kd = 24 nM 0J0 C22 H28 N5 O2 CN1c2ccccc....
5 3C79 Kd = 63 nM IM4 C9 H10 Cl N5 O2 c1cc(ncc1C....
6 2BYR Kd = 2.8 nM MLK C37 H50 N2 O10 CC[N@]1C[C....
7 4XHE - 40P C41 H61 N O9 C[C@H]1C[C....
8 2WNJ Kd = 330 nM ZY7 C19 H20 N2 O2 COc1ccc(c(....
9 2BYS Kd = 0.3 nM LOB C22 H27 N O2 C[N@@]1[C@....
10 2PGZ Kd = 1.8 uM COC C17 H21 N O4 C[N@]1[C@H....
11 2XNV Ki = 5 uM VU3 C21 H24 N2 c1ccc(cc1)....
12 5AIN - QMR C13 H13 N3 c1cnc2cc3c....
13 2WN9 Kd = 3 nM ZY5 C18 H18 N2 O2 COc1cc(ccc....
14 3C84 Kd = 14 nM TH4 C10 H9 Cl N4 S c1cc(ncc1C....
15 2XYS Ki = 38 nM SY9 C21 H22 N2 O2 c1ccc2c(c1....
16 4BFQ - 083 C21 H18 N6 Cc1cc(nc(n....
17 4XK9 - 41J C42 H63 N O7 C[C@H]1C[C....
18 2YME Kd = 549 nM CWB C18 H24 N4 O Cn1c2ccccc....
19 4QAC Kd = 0.0004 uM KK3 C17 H19 F3 N4 CC1CCN(CC1....
20 1UW6 Kd = 45.2 nM NCT C10 H14 N2 C[N@@]1CCC....
21 3WTM Kd = 0.1 uM N1Y C10 H11 Cl N4 O2 c1cc(ncc1C....
22 5J5G Kd = 0.03 uM 6GF C23 H22 N6 O COc1ccc(cc....
23 3WTN Kd = 0.091 uM N2Y C9 H11 Cl N4 [H]/N=C1/N....
24 4ALX Ki = 52 nM IZN C16 H21 N O3 CO[C@H]1CC....
25 1UV6 Kd = 7575 nM CCE C6 H15 N2 O2 C[N+](C)(C....
26 3ZDG Ki = 0.079 uM XRX C9 H20 N2 O2 C[C@H](CCO....
27 5J5I Kd = 0.13 uM 6GM C22 H20 N6 O c1ccnc(c1)....
28 5J5F Kd = 0.33 uM 6GH C20 H18 N6 S c1ccnc(c1)....
29 3ZDH Ki = 0.045 uM XRS C10 H19 N3 O C[C@H](CCO....
30 3WTL Kd = 0.092 uM N1Y C10 H11 Cl N4 O2 c1cc(ncc1C....
31 3WTO Kd = 0.119 uM N2Y C9 H11 Cl N4 [H]/N=C1/N....
32 3WTJ Kd = 0.297 uM TH4 C10 H9 Cl N4 S c1cc(ncc1C....
33 5AFH - L0B C22 H27 N O2 CN1[C@@H](....
34 5AFK ic50 = 132 uM 5VU C11 H12 F2 N2 O c1cc(c(cc1....
35 5AFN ic50 = 34 uM OJD C12 H15 N O c1ccc(cc1)....
36 5AFJ ic50 = 42 uM 42R C13 H14 Br N O2 C[C@@]1(CN....
37 5AFL ic50 = 398 uM FHV C12 H16 N2 O Cc1cccc(c1....
38 4UXU - MLK C37 H50 N2 O10 CC[N@]1C[C....
39 5LXB - 7A9 C19 H24 N2 O c1cc2c3c(c....
40 4ZJS - 4P0 C10 H15 N O CC(=O)C1=C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SRO; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 SRO 1 1
2 ASE 0.581818 0.785714
3 TSS 0.48 0.823529
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2bys.bio2) has 122 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2bys.bio2) has 122 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2bys.bio2) has 123 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found: 2
This union binding pocket(no: 4) in the query (biounit: 2bys.bio2) has 125 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2G30 ALA ALA PHE 0.002205 0.46658 6.60793
2 4AFH L0B 0.0000001551 0.70467 33.0396
Pocket No.: 5; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2bys.bio2) has 125 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2bys.bio1) has 144 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 2bys.bio1) has 140 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 2bys.bio1) has 147 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found: 3
This union binding pocket(no: 9) in the query (biounit: 2bys.bio1) has 150 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2XG5 EC5 0.02604 0.4647 5.50459
2 2XG5 EC2 0.02604 0.4647 5.50459
3 2VDF OCT 0.009302 0.47107 11.4537
Pocket No.: 10; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 2bys.bio1) has 145 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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