Receptor
PDB id Resolution Class Description Source Keywords
3CYZ 1.8 Å NON-ENZYME: BINDING DIMERIC CRYSTAL STRUCTURE OF A PHEROMONE BINDING PROTEIN FRO MELLIFERA IN COMPLEX WITH 9-KETO-2(E)-DECENOIC ACID AT PH 7 APIS MELLIFERA HONEYBEE APIS MELLIFERA PHEROMONE BINDING PROTEIN SIGNAL TRANSDUCTION QUEEN MANDIBULAR PHEROMONE
Ref.: QUEEN BEE PHEROMONE BINDING PROTEIN PH-INDUCED DOMA SWAPPING FAVORS PHEROMONE RELEASE J.MOL.BIOL. V. 390 981 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
9OD A:124;
B:121;
B:122;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 60 nM
184.232 C10 H16 O3 CC(=O...
CL A:120;
A:121;
A:122;
B:120;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
GOL B:123;
B:124;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MG A:123;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3D78 1.6 Å NON-ENZYME: BINDING DIMERIC CRYSTAL STRUCTURE OF A PHEROMONE BINDING PROTEIN MUTANT D35N, FROM APIS MELLIFERA, AT PH 7.0 APIS MELLIFERA PHEROMONE BINDING PROTEIN HONEY BEE APIS MELLIFERA SIGNALTRANSDUCTION QUEEN MANDIBULAR PROTEIN PH
Ref.: QUEEN BEE PHEROMONE BINDING PROTEIN PH-INDUCED DOMAIN SWAPPING FAVORS PHEROMONE RELEASE J.MOL.BIOL. V. 390 981 2009
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 552 families.
1 3BFB - 9OD C10 H16 O3 CC(=O)CCCC....
2 3D78 Kd = 23 nM NBB C10 H15 N O2 S CCCCNS(=O)....
3 3D74 - NBB C10 H15 N O2 S CCCCNS(=O)....
4 3CYZ Kd = 60 nM 9OD C10 H16 O3 CC(=O)CCCC....
5 3D75 - NBB C10 H15 N O2 S CCCCNS(=O)....
6 3BFH - PLM C16 H32 O2 CCCCCCCCCC....
7 3D76 Kd = 23 nM NBB C10 H15 N O2 S CCCCNS(=O)....
8 3BFA - 9OD C10 H16 O3 CC(=O)CCCC....
9 3D77 - NBB C10 H15 N O2 S CCCCNS(=O)....
10 3BJH - NBB C10 H15 N O2 S CCCCNS(=O)....
11 3CZ0 Kd = 60 nM 9OD C10 H16 O3 CC(=O)CCCC....
12 3CZ1 Kd = 55 nM NBB C10 H15 N O2 S CCCCNS(=O)....
13 3D73 - NBB C10 H15 N O2 S CCCCNS(=O)....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 426 families.
1 3BFB - 9OD C10 H16 O3 CC(=O)CCCC....
2 3D78 Kd = 23 nM NBB C10 H15 N O2 S CCCCNS(=O)....
3 3D74 - NBB C10 H15 N O2 S CCCCNS(=O)....
4 3CYZ Kd = 60 nM 9OD C10 H16 O3 CC(=O)CCCC....
5 3D75 - NBB C10 H15 N O2 S CCCCNS(=O)....
6 3BFH - PLM C16 H32 O2 CCCCCCCCCC....
7 3D76 Kd = 23 nM NBB C10 H15 N O2 S CCCCNS(=O)....
8 3BFA - 9OD C10 H16 O3 CC(=O)CCCC....
9 3D77 - NBB C10 H15 N O2 S CCCCNS(=O)....
10 3BJH - NBB C10 H15 N O2 S CCCCNS(=O)....
11 3CZ0 Kd = 60 nM 9OD C10 H16 O3 CC(=O)CCCC....
12 3CZ1 Kd = 55 nM NBB C10 H15 N O2 S CCCCNS(=O)....
13 3D73 - NBB C10 H15 N O2 S CCCCNS(=O)....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 families.
1 3BFB - 9OD C10 H16 O3 CC(=O)CCCC....
2 3D78 Kd = 23 nM NBB C10 H15 N O2 S CCCCNS(=O)....
3 3D74 - NBB C10 H15 N O2 S CCCCNS(=O)....
4 3CYZ Kd = 60 nM 9OD C10 H16 O3 CC(=O)CCCC....
5 3D75 - NBB C10 H15 N O2 S CCCCNS(=O)....
6 3BFH - PLM C16 H32 O2 CCCCCCCCCC....
7 3D76 Kd = 23 nM NBB C10 H15 N O2 S CCCCNS(=O)....
8 3BFA - 9OD C10 H16 O3 CC(=O)CCCC....
9 3D77 - NBB C10 H15 N O2 S CCCCNS(=O)....
10 3BJH - NBB C10 H15 N O2 S CCCCNS(=O)....
11 3CZ0 Kd = 60 nM 9OD C10 H16 O3 CC(=O)CCCC....
12 3CZ1 Kd = 55 nM NBB C10 H15 N O2 S CCCCNS(=O)....
13 3D73 - NBB C10 H15 N O2 S CCCCNS(=O)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 9OD; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 9OD 1 1
2 3X1 0.605263 0.73913
3 VCA 0.422222 0.72
4 PAM 0.422222 0.72
Similar Ligands (3D)
Ligand no: 1; Ligand: 9OD; Similar ligands found: 68
No: Ligand Similarity coefficient
1 AZ1 0.9416
2 DKA 0.9331
3 KAP 0.9294
4 GC7 0.9288
5 U4G 0.9247
6 Q9C 0.9188
7 OKP 0.9150
8 ZE7 0.9140
9 OKS 0.9137
10 5UF 0.9119
11 ALY 0.9094
12 8AC 0.9091
13 5D4 0.9070
14 BOW 0.9064
15 DNN 0.9061
16 HRG 0.9058
17 SS9 0.9015
18 D9L 0.9013
19 XS6 0.8998
20 11A 0.8973
21 DAO 0.8973
22 N8C 0.8971
23 KNA 0.8956
24 NOT 0.8940
25 1KJ 0.8932
26 SPD 0.8926
27 1PB 0.8909
28 REG 0.8889
29 NC4 0.8869
30 HZZ 0.8858
31 DXJ 0.8846
32 HPK 0.8839
33 HAR 0.8837
34 S0B 0.8819
35 TBJ 0.8811
36 MFY 0.8806
37 D10 0.8803
38 TEG 0.8803
39 NMM 0.8792
40 SZA 0.8788
41 4JK 0.8785
42 7XA 0.8783
43 DHJ 0.8776
44 HPX 0.8775
45 HJD 0.8769
46 ODI 0.8758
47 20P 0.8755
48 RPI 0.8747
49 19N 0.8737
50 MGB 0.8726
51 EXY 0.8724
52 PUW 0.8706
53 PHQ ALA 0.8689
54 DTB 0.8684
55 LPA 0.8681
56 DIA 0.8679
57 RED 0.8678
58 4DI 0.8661
59 LBY 0.8650
60 CT0 0.8631
61 IPJ 0.8625
62 0XR 0.8619
63 3CX 0.8612
64 PAO 0.8591
65 5PV 0.8591
66 D53 0.8585
67 HPL 0.8563
68 FXY 0.8547
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 3d78.bio3) has 50 residues
No: Leader PDB Ligand Sequence Similarity
1 6RQP OLC 4.20168
Pocket No.: 2; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 3d78.bio3) has 50 residues
No: Leader PDB Ligand Sequence Similarity
1 6RQP OLC 4.20168
Pocket No.: 3; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3d78.bio2) has 58 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3d78.bio1) has 58 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3d78.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3d78.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
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