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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 510 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 391 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 298 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: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 NBB 1 1
2 GG8 0.522727 0.823529
3 HS7 0.416667 0.645161
4 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 with APoc: 203
This union binding pocket(no: 1) in the query (biounit: 3d78.bio3) has 50 residues
No: Leader PDB Ligand Sequence Similarity
1 3O01 DXC None
2 1UO5 PIH None
3 5NNT DPV None
4 5X80 SAL None
5 1NU4 MLA None
6 3KP6 SAL None
7 1UO4 PIH None
8 1N13 AG2 None
9 2QQC AG2 None
10 4V1F BQ1 None
11 3O94 NCA None
12 4F4S EFO None
13 4RJD TFP None
14 5DCH 1YO None
15 1Q7E MET None
16 2YVE MBT None
17 1JAY F42 None
18 3E70 GDP None
19 1O4T OXL None
20 3NJQ NJQ None
21 1ZEI CRS None
22 5N0L ILE None
23 1MT1 AG2 None
24 4TR9 38D None
25 3P9T TCL None
26 5N8V KZZ None
27 4WG0 CHD None
28 3QP8 HL0 None
29 4C2G ALA ALA ALA ALA 1.68067
30 1WLJ U5P 1.68067
31 4CMI M4V 1.68067
32 4J26 EST 2.52101
33 2BVE PH5 2.52101
34 4J24 EST 2.52101
35 5K21 6QF 2.52101
36 1YYE 196 2.52101
37 5XJD 87L 2.52101
38 5J32 IPM 2.52101
39 3H9A PPY 2.88066
40 5URY PAM 3.36134
41 5C1M OLC 3.36134
42 1NF8 BOG 3.36134
43 3R9V DXC 3.36134
44 5UN9 NHT 3.36134
45 2BO4 FLC 3.36134
46 3ZQE DXC 3.36134
47 5C1M 4VO 3.36134
48 2QQD AG2 3.36134
49 3GXO MQA 3.36134
50 1Q19 SSC 3.36134
51 6FXR AKG 3.36134
52 3KO0 TFP 3.9604
53 5W7B MYR 4.20168
54 4REF 3N0 4.20168
55 5DNU KKN 4.20168
56 4A7W GTP 4.20168
57 4L77 CNL 4.20168
58 4RHS SIA SIA GAL 4.20168
59 4NTO 1PW 4.20168
60 2W9S TOP 4.20168
61 2CIX CEJ 4.20168
62 1ZPD CIT 4.20168
63 2OZ5 7XY 4.39189
64 5N18 8HZ 4.58716
65 1GEG GLC 5.04202
66 1ZED PNP 5.04202
67 5DXG EST 5.04202
68 4EAX S12 5.04202
69 4TV1 36M 5.04202
70 3TL1 JRO 5.04202
71 2Z5Y HRM 5.04202
72 4HBM 0Y7 5.04202
73 5DXE EST 5.04202
74 1YP0 PEF 5.04202
75 3BPX SAL 5.04202
76 3UU7 2OH 5.04202
77 3GYT DL4 5.04202
78 4POJ 2VP 5.04202
79 4M8E 29V 5.04202
80 1K2V DEF 5.04202
81 3N7S 3N7 5.21739
82 4OIC A8S 5.7971
83 4WGF HX2 5.88235
84 3ETG GTP 5.88235
85 4MRP GSH 5.88235
86 1S8G DAO 5.88235
87 2Z77 NCA 5.88235
88 5UNJ RJW 5.88235
89 3IWK NAD 5.88235
90 3ETG GWD 5.88235
91 3HYW DCQ 5.88235
92 2UYP PPI 5.88235
93 3H4L ANP 5.88235
94 4DK7 0KS 5.88235
95 1J78 OLA 5.88235
96 2UYN 2KT 5.88235
97 1Y75 NAG 5.9322
98 2HPL ASP ASP LEU TYR GLY 6
99 5EE7 5MV 6.72269
100 1J71 THR ILE THR SER 6.72269
101 2D5X L35 6.72269
102 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 6.72269
103 2WT9 NIO 6.72269
104 1KYZ FER 6.72269
105 4RYV ZEA 6.72269
106 6G5J EM8 6.72269
107 3GUZ PAF 6.72269
108 6BR8 6OU 6.72269
109 1Q5D EPB 6.72269
110 5FS0 5JC 6.72269
111 3OQJ 3CX 6.72269
112 6H8S FSZ 6.72269
113 2VCN ISZ 6.72269
114 4FFG 0U8 6.72269
115 4ZBR NPS 6.72269
116 1RV1 IMZ 7.05882
117 4OFJ HIS 7.56302
118 5M36 9SZ 7.56302
119 3AQT RCO 7.56302
120 5OSW DIU 7.56302
121 5OWC AYZ 7.56302
122 5SYM 71Q 7.56302
123 4C1M NIH 7.56302
124 2IZ1 ATR 7.56302
125 1XK9 P34 7.56302
126 3RV5 DXC 7.86517
127 5X5M 7YU 7.87037
128 6AZQ C5J 8.40336
129 5CX8 TG6 8.40336
130 6C0B PAM 8.40336
131 1ZDT PEF 8.40336
132 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 8.57143
133 4DE2 DN3 9.2437
134 5FPN KYD 9.2437
135 2GL0 ADN 9.2437
136 1KTG AMP 9.2437
137 4RHP PEF 9.2437
138 4ARE FLC 9.2437
139 3F8C HT1 9.2437
140 5CKW ANP 9.2437
141 4TSZ ACE GLN ALC ASP LEU ZCL 9.2437
142 2WG9 OCA 9.2437
143 3RMK BML 9.63855
144 3RET SAL 9.90099
145 3RET PYR 9.90099
146 4DS0 A2G GAL NAG FUC 10.084
147 5LX9 OLB 10.084
148 4RW3 TDA 10.084
149 5LWY OLB 10.084
150 3OJI PYV 10.084
151 4DS8 A8S 10.084
152 4XNV BUR 10.084
153 3KDJ A8S 10.084
154 2JC9 ADN 10.084
155 2PFC PLM 10.084
156 3JRS A8S 10.084
157 5JO1 6LM 10.084
158 5Z84 CHD 10.7143
159 5ZCO CHD 10.7143
160 5W97 CHD 10.7143
161 2DYR TGL 10.7143
162 3TDC 0EU 10.9244
163 6GMN F4E 10.9244
164 2Y69 CHD 11.7647
165 1DQE BOM 11.7647
166 2IDO TMP 12.605
167 4R29 SAM 12.605
168 4MGA 27L 13.4454
169 2P3I MNA 13.4454
170 5HYR EST 13.4454
171 4MGB XDH 13.4454
172 4MG9 27K 13.4454
173 5DX3 EST 13.4454
174 1C1X HFA 13.4454
175 3UUD EST 13.4454
176 5WGD EST 13.4454
177 1BW9 PPY 13.4454
178 2QZO KN1 13.4454
179 1M2Z BOG 14.2857
180 6C1R EFD 14.2857
181 2GBB CIT 14.2857
182 4P6X HCY 14.2857
183 3NMV PYV 15.126
184 4OGQ 2WD 15.9664
185 4OGQ 1O2 15.9664
186 4OGQ 7PH 15.9664
187 5C9J DAO 15.9664
188 6A0S NDP 16.8067
189 3TKY N7I 16.8067
190 2UW1 GVM 17.6471
191 5XNA SHV 17.6471
192 5TVI MYR 18.4783
193 3RY9 1CA 18.4874
194 4E2J MOF 18.4874
195 4RKK GLC GLC GLC GLC GLC GLC 18.4874
196 2Q1H AS4 18.4874
197 4V3I ASP LEU THR ARG PRO 19.3277
198 3HRD NIO 22.6891
199 3S0E EOL 24.3697
200 5UGW GSH 26.0504
201 1XMY ROL 27.7311
202 4LO6 SIA GAL 29.4118
203 1OW4 2AN 33.6134
Pocket No.: 2; 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: 2) in the query (biounit: 3d78.bio3) has 50 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found with APoc: 63
This union binding pocket(no: 3) in the query (biounit: 3d78.bio2) has 58 residues
No: Leader PDB Ligand Sequence Similarity
1 2Q37 3AL None
2 5ET3 60C None
3 1UI0 URA None
4 3AQA BYH None
5 5X3R 7Y3 None
6 4K7O EKZ None
7 2Z9I GLY ALA THR VAL 0.617284
8 5C1M CLR 3.36134
9 1QV1 CZH 3.36134
10 5LXB 7A9 3.36134
11 6BVL EBY 4.20168
12 6BVJ EAS 4.20168
13 6BVI EC4 4.20168
14 1R6N 434 4.20168
15 1HG4 LPP 4.20168
16 1YUC EPH 4.20168
17 2PNC CLU 4.20168
18 1Y7P RIP 4.20168
19 2WVZ KIF 4.20168
20 5FII PHE 4.90196
21 4O4Z N2O 5.04202
22 4URG C2E 5.04202
23 2YLD CMO 5.04202
24 5CQG 55C 5.04202
25 3O5N BR0 5.35714
26 5XKR BZE 5.88235
27 1SGJ OAA 5.88235
28 1YOK P6L 5.88235
29 6BR8 PGV 6.72269
30 3W54 RNB 6.72269
31 3DTU DXC 6.72269
32 1G0N NDP 6.72269
33 1G0N PHH 6.72269
34 4OHU NAD 6.72269
35 4OHU 2TK 6.72269
36 4CNK MEU 7.56302
37 1QHO MAL 8.40336
38 5I8F ML1 9.2437
39 2CXG GLC GLC 9.2437
40 1MAI I3P 9.2437
41 3QTP 2PG 9.2437
42 4DE3 DN8 9.2437
43 1XVB BHL 10.084
44 5HWK BEZ 10.084
45 1XVB BHL BHL 10.084
46 4ORM 2V6 10.9244
47 4ORM FMN 10.9244
48 4ORM ORO 10.9244
49 4NZ6 DLY 10.9244
50 5T96 79J 11.7647
51 1TV5 N8E 11.7647
52 5WHU SIA GAL GLC 12.605
53 3I27 SID 12.605
54 5X20 AOT 13.4454
55 5WGQ EST 13.4454
56 3R9C ECL 13.4454
57 1KQR MNA 13.4454
58 4MG7 27H 13.4454
59 1YVZ JPC 15.9664
60 1Q8A HCS 15.9664
61 5T9C G3P 15.9664
62 1VG0 GER 17.6471
63 4LH7 1X8 19.3277
Pocket No.: 4; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found with APoc: 8
This union binding pocket(no: 4) in the query (biounit: 3d78.bio1) has 58 residues
No: Leader PDB Ligand Sequence Similarity
1 4DOL PLM None
2 3T03 3T0 1.68067
3 5GZK BGC 4.20168
4 3B9Z CO2 5.88235
5 1PZL MYR 7.56302
6 1Y0L HAN 13.4454
7 5X4Q 7Z6 18.4874
8 3G58 988 29.4118
Pocket No.: 5; Query (leader) PDB : 3D78; Ligand: NBB; Similar sites found with APoc: 5
This union binding pocket(no: 5) in the query (biounit: 3d78.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
1 5E70 RCD 3.36134
2 3RGA ILD 5.04202
3 2W3L DRO 5.88235
4 2DYS TGL 10.7143
5 1ZGA HMK 10.9244
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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