Receptor
PDB id Resolution Class Description Source Keywords
2yme 2.4 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF A MUTANT BINDING PROTEIN (5HTBP-ACHBP) WITH GRANISETRON APLYSIA CALIFORNICA RECEPTOR PENTAMERIC LIGAND-GATED ION CHANNEL
Ref.: STRUCTURAL BASIS OF LIGAND RECOGNITION IN 5-HT3 REC EMBO REP. V. 14 49 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CWB A:1207;
B:1207;
C:1207;
D:1207;
E:1207;
F:1207;
G:1207;
H:1207;
I:1207;
J:1207;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 Kd = 343 uM
312.409 C18 H24 N4 O Cn1c2...
NA I:1208;
 Invalid;
 none;
 submit data
22.99 Na [Na+]
NAG A:1206;
B:1206;
C:1206;
D:1208;
E:1209;
F:1206;
H:1206;
I:1206;
J:1206;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
221.208 C8 H15 N O6 CC(=O...
PO4 A:1208;
C:1208;
E:1208;
G:1208;
H:1208;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
94.971 O4 P [O-]P...
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 COMPL LOBELINE APLYSIA CALIFORNICA ACETYLCHOLINE BINDING PROTEIN NICOTINIC ACETYLCHOLINE CONFORMATIONAL FLEXIBILITY LOBELINE RECEPTOR
Ref.: STRUCTURES OF APLYSIA ACHBP COMPLEXES WITH NICOTINI 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 289 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 = 343 uM 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 214 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 = 343 uM 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 (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 2WNC Kd = 479 nM TKT C17 H20 N2 O2 CN1[C@H]2C....
2 4DBM Kd = 24 nM 0J0 C22 H28 N5 O2 CN1c2ccccc....
3 3C79 Kd = 63 nM IM4 C9 H10 Cl N5 O2 c1cc(ncc1C....
4 2BYR Kd = 2.8 nM MLK C37 H50 N2 O10 CC[N@]1C[C....
5 4XHE - 40P C41 H61 N O9 C[C@H]1C[C....
6 2WNJ Kd = 330 nM ZY7 C19 H20 N2 O2 COc1ccc(c(....
7 2BYS Kd = 0.3 nM LOB C22 H27 N O2 C[N@@]1[C@....
8 2PGZ Kd = 1.8 uM COC C17 H21 N O4 C[N@]1[C@H....
9 2XNV Ki = 5 uM VU3 C21 H24 N2 c1ccc(cc1)....
10 5AIN - QMR C13 H13 N3 c1cnc2cc3c....
11 2WN9 Kd = 3 nM ZY5 C18 H18 N2 O2 COc1cc(ccc....
12 3C84 Kd = 14 nM TH4 C10 H9 Cl N4 S c1cc(ncc1C....
13 2XYS Ki = 38 nM SY9 C21 H22 N2 O2 c1ccc2c(c1....
14 4BFQ - 083 C21 H18 N6 Cc1cc(nc(n....
15 4XK9 - 41J C42 H63 N O7 C[C@H]1C[C....
16 2YME Kd = 343 uM CWB C18 H24 N4 O Cn1c2ccccc....
17 3ZDG Ki = 0.079 uM XRX C9 H20 N2 O2 C[C@H](CCO....
18 5J5I Kd = 0.13 uM 6GM C22 H20 N6 O c1ccnc(c1)....
19 5J5F Kd = 0.33 uM 6GH C20 H18 N6 S c1ccnc(c1)....
20 3ZDH Ki = 0.045 uM XRS C10 H19 N3 O C[C@H](CCO....
21 3WTL Kd = 0.092 uM N1Y C10 H11 Cl N4 O2 c1cc(ncc1C....
22 3WTO Kd = 0.119 uM N2Y C9 H11 Cl N4 [H]/N=C1/N....
23 3WTJ Kd = 0.297 uM TH4 C10 H9 Cl N4 S c1cc(ncc1C....
24 5AFJ ic50 = 42 uM 42R C13 H14 Br N O2 C[C@@]1(CN....
25 5AFL ic50 = 398 uM FHV C12 H16 N2 O Cc1cccc(c1....
26 5LXB - 7A9 C19 H24 N2 O c1cc2c3c(c....
27 4ZJS - 4P0 C10 H15 N O CC(=O)C1=C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: CWB; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 CWB 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: CWB; Similar ligands found: 16
No: Ligand Similarity coefficient
1 TKT 0.9618
2 31F 0.8853
3 5XM 0.8818
4 65W 0.8783
5 4YE 0.8753
6 29F 0.8706
7 06R 0.8699
8 GN5 0.8637
9 8M5 0.8631
10 651 0.8627
11 J5Z 0.8604
12 ZW2 0.8591
13 XAV 0.8567
14 A64 0.8557
15 1V8 0.8557
16 8WW 0.8534
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 2bys.bio2) has 122 residues
No: Leader PDB Ligand Sequence Similarity
1 4AFH L0B 33.0396
2 4AFH L0B 33.0396
3 4AFH L0B 33.0396
4 4AFH L0B 33.0396
5 4AFH L0B 33.0396
Pocket No.: 2; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found with APoc: 4
This union binding pocket(no: 2) in the query (biounit: 2bys.bio2) has 122 residues
No: Leader PDB Ligand Sequence Similarity
1 4AFH L0B 33.0396
2 4AFH L0B 33.0396
3 4AFH L0B 33.0396
4 4AFH L0B 33.0396
Pocket No.: 3; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found with APoc: 4
This union binding pocket(no: 3) in the query (biounit: 2bys.bio2) has 123 residues
No: Leader PDB Ligand Sequence Similarity
1 4AFH L0B 33.0396
2 4AFH L0B 33.0396
3 4AFH L0B 33.0396
4 4AFH L0B 33.0396
Pocket No.: 4; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found with APoc: 4
This union binding pocket(no: 4) in the query (biounit: 2bys.bio2) has 125 residues
No: Leader PDB Ligand Sequence Similarity
1 4AFH L0B 33.0396
2 4AFH L0B 33.0396
3 4AFH L0B 33.0396
4 4AFH L0B 33.0396
Pocket No.: 5; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found with APoc: 4
This union binding pocket(no: 5) in the query (biounit: 2bys.bio2) has 125 residues
No: Leader PDB Ligand Sequence Similarity
1 4AFH L0B 33.0396
2 4AFH L0B 33.0396
3 4AFH L0B 33.0396
4 4AFH L0B 33.0396
Pocket No.: 6; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found with APoc: 5
This union binding pocket(no: 6) in the query (biounit: 2bys.bio1) has 144 residues
No: Leader PDB Ligand Sequence Similarity
1 4AFH L0B 33.0396
2 4AFH L0B 33.0396
3 4AFH L0B 33.0396
4 4AFH L0B 33.0396
5 4AFH L0B 33.0396
Pocket No.: 7; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found with APoc: 2
This union binding pocket(no: 7) in the query (biounit: 2bys.bio1) has 140 residues
No: Leader PDB Ligand Sequence Similarity
1 4AFH L0B 33.0396
2 4AFH L0B 33.0396
Pocket No.: 8; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found with APoc: 5
This union binding pocket(no: 8) in the query (biounit: 2bys.bio1) has 147 residues
No: Leader PDB Ligand Sequence Similarity
1 4AFH L0B 33.0396
2 4AFH L0B 33.0396
3 4AFH L0B 33.0396
4 4AFH L0B 33.0396
5 4AFH L0B 33.0396
Pocket No.: 9; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found with APoc: 2
This union binding pocket(no: 9) in the query (biounit: 2bys.bio1) has 150 residues
No: Leader PDB Ligand Sequence Similarity
1 4AFH L0B 33.0396
2 4AFH L0B 33.0396
Pocket No.: 10; Query (leader) PDB : 2BYS; Ligand: LOB; Similar sites found with APoc: 5
This union binding pocket(no: 10) in the query (biounit: 2bys.bio1) has 145 residues
No: Leader PDB Ligand Sequence Similarity
1 4AFH L0B 33.0396
2 4AFH L0B 33.0396
3 4AFH L0B 33.0396
4 4AFH L0B 33.0396
5 4AFH L0B 33.0396
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