PDB
6N48
Resolution
3.2 Å
Released
June 26, 2019
Receptor
β2
Class
A
Species
Homo sapiens
Ligands
Function
Nanobody 6B9
Allosteric agonist
CHEMBL1615159
Agonist
compound-6FA
PAM
Reference
10.1126/SCIENCE.AAW8981
Nanobody 6B9 CHEMBL1615159 compound-6FA

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Ligand Amino Acid Generic Number Segment Interaction Type
Nanobody 6B9 T1068 2.39x39 TM2 Van der Waals
compound-6FA F1071 2.42x42 TM2 Van der Waals
CHEMBL1615159 W1109 3.28x28 TM3 hydrophobic
CHEMBL1615159 T1110 3.29x29 TM3 hydrophobic
CHEMBL1615159 D1113 3.32x32 TM3 polar (charge-charge)
CHEMBL1615159 D1113 3.32x32 TM3 polar (hydrogen bond)
CHEMBL1615159 V1114 3.33x33 TM3 hydrophobic
CHEMBL1615159 V1117 3.36x36 TM3 hydrophobic
compound-6FA V1126 3.45x45 TM3 Van der Waals
compound-6FA V1129 3.48x48 TM3 Van der Waals
compound-6FA D1130 3.49x49 TM3 Van der Waals
Nanobody 6B9 R1131 3.50x50 TM3 aromatic (pi-cation)
Nanobody 6B9 R1131 3.50x50 TM3 polar (hydrogen bond)
compound-6FA F1133 3.52x52 TM3 hydrophobic
compound-6FA F1133 3.52x52 TM3 aromatic (edge-to-face)
Nanobody 6B9 A1134 3.53x53 TM3 Van der Waals
Nanobody 6B9 I1135 3.54x54 TM3 polar (hydrogen bond with backbone)
Nanobody 6B9 I1135 3.54x54 TM3 hydrophobic
Nanobody 6B9 T1136 3.55x55 TM3 Van der Waals
compound-6FA S1137 3.56x56 TM3 Van der Waals
Nanobody 6B9 P1138 34.50x50 ICL2 hydrophobic
Nanobody 6B9 F1139 34.51x51 ICL2 hydrophobic
compound-6FA Y1141 34.53x53 ICL2 hydrophobic
compound-6FA L1144 34.56x56 ICL2 hydrophobic
compound-6FA L1145 34.57x57 ICL2 hydrophobic
compound-6FA K1149 4.41x41 TM4 polar (hydrogen bond)
compound-6FA V1152 4.44x44 TM4 hydrophobic
compound-6FA I1153 4.45x45 TM4 hydrophobic
compound-6FA M1156 4.48x48 TM4 Van der Waals
CHEMBL1615159 C1191 45.50x50 ECL2 Van der Waals
CHEMBL1615159 D1192 45.51x51 ECL2 Van der Waals
CHEMBL1615159 F1193 45.52x52 ECL2 hydrophobic
CHEMBL1615159 F1193 45.52x52 ECL2 aromatic (pi-cation)
CHEMBL1615159 A1200 5.39x40 TM5 Van der Waals
CHEMBL1615159 S1203 5.42x43 TM5 polar (hydrogen bond)
CHEMBL1615159 S1207 5.46x461 TM5 polar (hydrogen bond)
Nanobody 6B9 Y1219 5.58x58 TM5 hydrophobic
Nanobody 6B9 E1225 5.64x64 TM5 Van der Waals
Nanobody 6B9 A1226 5.65x65 TM5 hydrophobic
Nanobody 6B9 Q1229 ICL3 polar (hydrogen bond)
Nanobody 6B9 L1230 ICL3 Van der Waals
Nanobody 6B9 A1265 6.27x27 TM6 Van der Waals
Nanobody 6B9 K1267 6.29x29 TM6 polar (charge-charge)
Nanobody 6B9 K1267 6.29x29 TM6 hydrophobic
Nanobody 6B9 K1267 6.29x29 TM6 polar (hydrogen bond)
Nanobody 6B9 E1268 6.30x30 TM6 Van der Waals
Nanobody 6B9 A1271 6.33x33 TM6 hydrophobic
Nanobody 6B9 T1274 6.36x36 TM6 Van der Waals
Nanobody 6B9 L1275 6.37x37 TM6 Van der Waals
Nanobody 6B9 I1278 6.40x40 TM6 hydrophobic
CHEMBL1615159 W1286 6.48x48 TM6 Van der Waals
CHEMBL1615159 F1289 6.51x51 TM6 hydrophobic
CHEMBL1615159 F1290 6.52x52 TM6 aromatic (edge-to-face)
CHEMBL1615159 F1290 6.52x52 TM6 hydrophobic
CHEMBL1615159 N1293 6.55x55 TM6 polar (hydrogen bond)
CHEMBL1615159 Y1308 7.35x34 TM7 Van der Waals
CHEMBL1615159 I1309 7.36x35 TM7 hydrophobic
CHEMBL1615159 N1312 7.39x38 TM7 polar (hydrogen bond)
CHEMBL1615159 N1312 7.39x38 TM7 polar (hydrogen bond)
CHEMBL1615159 Y1316 7.43x42 TM7 polar (hydrogen bond)
Nanobody 6B9 Y1326 ICL4 hydrophobic
Nanobody 6B9 R1328 ICL4 hydrophobic
Nanobody 6B9 S1329 8.47x47 H8 Van der Waals
Nanobody 6B9 P1330 8.48x48 H8 hydrophobic

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Snake plot — Download: PNG | SVG
ICL1 E R L Q ICL1ECL1 M W T F ECL1ICL2 P F K Y Q S L L ICL2ECL2 W Y R A T H Q E A I N C Y A N E T C C D F F T ECL2ICL3 G R F H V Q N L S Q V E Q D G R T G H G L R R S ICL3ECL3 D N L I ECL3N-term M G Q P G N G S A F L L A P N G S H A P D H D V T N-termC-term L R R S S L K A Y G N G Y S S N G N T G E Q S G Y H V E Q E K E N K L L C E D L P G T E D F V G H Q G T V P S D N I D S Q G R N C S T N D S L L C-term Q E R D E V W V V G M G I V M S L I V L A I V F G N V L V I T A I A K F T V T N Y F I T S L A C A D L V M G L A V V P F G A A H I L M K G N F W C E F W T S I D V L C V T A S I E T L C V I A V D R Y F A I T S T K N K A R V I I L M V W I V S G L T S F L P I Q M H N Q A Y A I A S S I V S F Y V P L V I M V F V Y S R V F Q E A K R Q L Q K I D K S E S K F C L K E H K A L K T L G I I M G T F T L C W L P F F I V N I V H V I Q R K E V Y I L L N W I G Y V N S G F N P L I Y C R S P D F Q E F R I A L L C
Helix box plot — Download: PNG | SVG V N G F V I A L V I L S M V I G M G V V 1 T S L A C A D L V M G A L V V P F G A A H 2 V C L T E I S A T V C L V D I S T W F E 3 A R V I I L M V W I V S G L T S F L P I 4 Y V F V M I V L P V Y F S V I S S A I A Y 5 G I I M G T F T L C W L P F F I V N I V 6 L P N F G S N V Y G I W N L L I Y V E 7

GPCRdb(A)
GPCRdb(A)
β2-adrenoceptor
TM2
2x39 2.39x39 T68
2x42 2.42x42 F71
TM3
3x28 3.28x28 W109
3x29 3.29x29 T110
3x32 3.32x32 D113
3x33 3.33x33 V114
3x36 3.36x36 V117
3x45 3.45x45 V126
3x48 3.48x48 V129
3x49 3.49x49 D130
3x50 3.50x50 R131
3x52 3.52x52 F133
3x53 3.53x53 A134
3x54 3.54x54 I135
3x55 3.55x55 T136
3x56 3.56x56 S137
ICL2
34x50 34.50x50 P138
34x51 34.51x51 F139
34x53 34.53x53 Y141
34x56 34.56x56 L144
34x57 34.57x57 L145
TM4
4x41 4.41x41 K149
4x44 4.44x44 V152
4x45 4.45x45 I153
4x48 4.48x48 M156
ECL2
45x50 45.50x50 C191
45x51 45.51x51 D192
45x52 45.52x52 F193
TM5
5x40 5.39x40 A200
5x43 5.42x43 S203
5x461 5.46x461 S207
5x58 5.58x58 Y219
5x64 5.64x64 E225
5x65 5.65x65 A226
TM6
6x27 6.27x27 C265
6x29 6.29x29 K267
6x30 6.30x30 E268
6x33 6.33x33 A271
6x36 6.36x36 T274
6x37 6.37x37 L275
6x40 6.40x40 I278
6x48 6.48x48 W286
6x51 6.51x51 F289
6x52 6.52x52 F290
6x55 6.55x55 N293
TM7
7x34 7.35x34 Y308
7x35 7.36x35 I309
7x38 7.39x38 N312
7x42 7.43x42 Y316
H8
8x47 8.47x47 S329
8x48 8.48x48 P330