Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:121;
A:122;
A:123;
A:124;
A:125;
B:122;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
NBB A:120;
B:120;
B:121;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 23 nM
213.297 C10 H15 N O2 S CCCCN...
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 473 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 355 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 272 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
Ligand no: 1; Ligand: NBB; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 NBB 1 1
2 HS7 0.416667 0.645161
3 A09 0.4 0.607143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found: 37
This union binding pocket(no: 1) in the query (biounit: 3d78.bio3) has 50 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KP6 SAL 0.007816 0.45705 None
2 1N13 AG2 0.006657 0.45342 None
3 5DCH 1YO 0.01926 0.42744 None
4 4J8T DOG 0.02517 0.4076 None
5 3P9T TCL 0.03179 0.40597 None
6 2BVE PH5 0.01768 0.42 2.52101
7 3R9V DXC 0.02593 0.42001 3.36134
8 2QQD AG2 0.03252 0.41316 3.36134
9 4A7W GTP 0.02651 0.41931 4.20168
10 4RHS SIA SIA GAL 0.04442 0.4141 4.20168
11 5N18 8HZ 0.04674 0.40079 4.58716
12 1GEG GLC 0.01829 0.42832 5.04202
13 4EAX S12 0.03017 0.42118 5.04202
14 2Z5Y HRM 0.02156 0.41865 5.04202
15 1YP0 PEF 0.006044 0.41397 5.04202
16 3BPX SAL 0.04224 0.40821 5.04202
17 3GYT DL4 0.008231 0.40532 5.04202
18 3N7S 3N7 0.001963 0.492 5.21739
19 4DK7 0KS 0.01128 0.41109 5.88235
20 1Y75 NAG 0.04401 0.40217 5.9322
21 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 0.01457 0.43876 6.72269
22 1KYZ FER 0.02991 0.41767 6.72269
23 1KTG AMP 0.0209 0.42118 9.2437
24 2WH8 II2 0.02029 0.41607 9.2437
25 3RET SAL 0.02003 0.40909 9.90099
26 3RET PYR 0.02003 0.40909 9.90099
27 4DS0 A2G GAL NAG FUC 0.01136 0.44828 10.084
28 5LX9 OLB 0.005023 0.43859 10.084
29 4RW3 TDA 0.01965 0.43767 10.084
30 4XNV BUR 0.02796 0.41887 10.084
31 1DQE BOM 0.006822 0.41785 11.7647
32 2IDO TMP 0.01195 0.44029 12.605
33 4MGA 27L 0.04234 0.41524 13.4454
34 3RY9 1CA 0.01746 0.4054 18.4874
35 4E2J MOF 0.01128 0.40503 18.4874
36 4V3I ASP LEU THR ARG PRO 0.02165 0.42671 19.3277
37 1OW4 2AN 0.006495 0.44151 33.6134
Pocket No.: 2; Query (leader) PDB : 3D78; Ligand: NBB; 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: 3d78.bio3) has 50 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found: 39
This union binding pocket(no: 3) in the query (biounit: 3d78.bio2) has 58 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.003047 0.48345 None
2 2QQC AG2 0.003333 0.45413 None
3 2Q37 3AL 0.01047 0.42614 None
4 4K7O EKZ 0.02155 0.40032 None
5 2Z9I GLY ALA THR VAL 0.02783 0.40461 0.617284
6 4Q0K GA3 0.01441 0.40168 2.52101
7 1QV1 CZH 0.007086 0.40343 3.36134
8 3KO0 TFP 0.03213 0.40427 3.9604
9 2PNC CLU 0.02441 0.40266 4.20168
10 2WVZ KIF 0.01775 0.40101 4.20168
11 4URG C2E 0.01769 0.41189 5.04202
12 2YLD CMO 0.03515 0.40374 5.04202
13 4O4Z N2O 0.01481 0.40227 5.04202
14 4MRP GSH 0.02405 0.42373 5.88235
15 1SGJ OAA 0.01653 0.40702 5.88235
16 1YOK P6L 0.01143 0.40304 5.88235
17 3DTU DXC 0.03019 0.40713 6.72269
18 4TWP AXI 0.02625 0.4066 6.72269
19 1G0N PHH 0.01306 0.40645 6.72269
20 3AQT RCO 0.01679 0.41779 7.56302
21 4C1M NIH 0.02527 0.40766 7.56302
22 3KRR DQX 0.02536 0.40608 7.56302
23 5IXJ THR 0.006924 0.40654 8.40336
24 2YOR MZ0 0.0002144 0.48162 9.2437
25 1MAI I3P 0.02613 0.40691 9.2437
26 1XVB BHL BHL 0.03035 0.40013 10.084
27 4ORM FMN 0.02146 0.41071 10.9244
28 4ORM 2V6 0.02146 0.41071 10.9244
29 4ORM ORO 0.02146 0.41071 10.9244
30 4NZ6 DLY 0.0241 0.40755 10.9244
31 2Q8H TF4 0.01887 0.40434 10.9244
32 1TV5 N8E 0.02124 0.40915 11.7647
33 5T96 79J 0.03918 0.40298 11.7647
34 4R29 SAM 0.01116 0.41906 12.605
35 3I27 SID 0.03103 0.40056 12.605
36 1KQR MNA 0.02451 0.40431 13.4454
37 1Q8A HCS 0.021 0.4121 15.9664
38 4LH7 1X8 0.0123 0.42204 19.3277
39 3S0E EOL 0.0002779 0.42389 24.3697
Pocket No.: 4; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found: 16
This union binding pocket(no: 4) in the query (biounit: 3d78.bio1) has 58 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VWA PTY 0.00741 0.48042 None
2 4J26 EST 0.02735 0.4243 2.52101
3 1YYE 196 0.03225 0.41716 2.52101
4 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.01244 0.47099 5.88235
5 3HYW DCQ 0.01759 0.4474 5.88235
6 3B9Z CO2 0.03573 0.42936 5.88235
7 1J71 THR ILE THR SER 0.02475 0.44055 6.72269
8 1XK9 P34 0.03713 0.40523 7.56302
9 1ZDT PEF 0.01512 0.41079 8.40336
10 3K3K A8S 0.01427 0.42272 10.084
11 3KDJ A8S 0.01822 0.42051 10.084
12 4DS8 A8S 0.03071 0.41828 10.084
13 3TDC 0EU 0.004144 0.5124 10.9244
14 1ZGA HMK 0.03122 0.42122 10.9244
15 5X4Q 7Z6 0.02408 0.42726 18.4874
16 3G58 988 0.04347 0.40451 29.4118
Pocket No.: 5; Query (leader) PDB : 3D78; Ligand: NBB; 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: 3d78.bio1) has 50 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3D78; Ligand: NBB; 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: 3d78.bio1) has 50 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback