PDB
9UCP
Resolution
2.9 Å
Released
Oct. 29, 2025
Receptor
M1
Class
A
Species
Homo sapiens
Ligands
Function
Nanobody Nb1B4
Allosteric agonist
iperoxo
Agonist
Reference
10.1073/PNAS.2508879122
Nanobody Nb1B4 iperoxo

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Ligand Amino Acid Generic Number Segment Interaction Type
Nanobody Nb1B4 Y82 2.61x60 TM2 polar (hydrogen bond)
Nanobody Nb1B4 Y85 2.64x63 TM2 aromatic (edge-to-face)
Nanobody Nb1B4 Y85 2.64x63 TM2 hydrophobic
Nanobody Nb1B4 Y85 2.64x63 TM2 polar (hydrogen bond)
Nanobody Nb1B4 L86 2.65x64 TM2 hydrophobic
Nanobody Nb1B4 L87 2.66x65 TM2 Van der Waals
Nanobody Nb1B4 M88 2.67x66 TM2 Van der Waals
Nanobody Nb1B4 G89 2.68x67 TM2 Van der Waals
Nanobody Nb1B4 H90 23.49x49 ECL1 aromatic (edge-to-face)
Nanobody Nb1B4 H90 23.49x49 ECL1 polar (hydrogen bond)
Nanobody Nb1B4 H90 23.49x49 ECL1 polar (hydrogen bond)
iperoxo D105 3.32x32 TM3 Van der Waals
iperoxo Y106 3.33x33 TM3 aromatic (pi-cation)
iperoxo Y106 3.33x33 TM3 hydrophobic
iperoxo S109 3.36x36 TM3 Van der Waals
iperoxo N110 3.37x37 TM3 Van der Waals
iperoxo V113 3.40x40 TM3 hydrophobic
iperoxo W157 4.57x57 TM4 Van der Waals
Nanobody Nb1B4 T172 ECL2 polar (hydrogen bond with backbone)
Nanobody Nb1B4 L174 ECL2 hydrophobic
Nanobody Nb1B4 A175 ECL2 polar (hydrogen bond with backbone)
Nanobody Nb1B4 A175 ECL2 hydrophobic
Nanobody Nb1B4 G176 ECL2 Van der Waals
Nanobody Nb1B4 Q177 ECL2 hydrophobic
Nanobody Nb1B4 Y179 45.51x51 ECL2 hydrophobic
Nanobody Nb1B4 Y179 45.51x51 ECL2 polar (hydrogen bond)
Nanobody Nb1B4 L183 ECL2 hydrophobic
Nanobody Nb1B4 S184 ECL2 Van der Waals
iperoxo A196 5.46x461 TM5 Van der Waals
iperoxo F197 5.47x47 TM5 Van der Waals
iperoxo W338 6.48x48 TM6 hydrophobic
iperoxo Y341 6.51x51 TM6 aromatic (pi-cation)
iperoxo N342 6.52x52 TM6 Van der Waals
Nanobody Nb1B4 M344 6.54x54 TM6 Van der Waals
Nanobody Nb1B4 V345 6.55x55 TM6 Van der Waals
Nanobody Nb1B4 S348 6.58x58 TM6 polar (hydrogen bond)
Nanobody Nb1B4 K352 ECL3 hydrophobic
Nanobody Nb1B4 D353 ECL3 Van der Waals
Nanobody Nb1B4 V355 ECL3 Van der Waals
Nanobody Nb1B4 P356 7.31x30 TM7 Van der Waals
Nanobody Nb1B4 E357 7.32x31 TM7 hydrophobic
Nanobody Nb1B4 W360 7.35x34 TM7 aromatic (pi-cation)
Nanobody Nb1B4 W360 7.35x34 TM7 aromatic (edge-to-face)
Nanobody Nb1B4 E361 7.36x35 TM7 polar (hydrogen bond)
Nanobody Nb1B4 Y364 7.39x38 TM7 hydrophobic
iperoxo Y364 7.39x38 TM7 aromatic (pi-cation)
iperoxo C367 7.42x41 TM7 Van der Waals
iperoxo Y368 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
M1 receptor
TM2
2x60 2.61x60 Y82
2x63 2.64x63 Y85
2x64 2.65x64 L86
2x65 2.66x65 L87
2x66 2.67x66 M88
2x67 2.68x67 G89
ECL1
23x49 23.49x49 H90
TM3
3x32 3.32x32 D105
3x33 3.33x33 Y106
3x36 3.36x36 S109
3x37 3.37x37 N110
3x40 3.40x40 V113
TM4
4x57 4.57x57 W157
ECL2
45x51 45.51x51 Y179
TM5
5x461 5.46x461 A196
5x47 5.47x47 F197
TM6
6x48 6.48x48 W378
6x51 6.51x51 Y381
6x52 6.52x52 N382
6x54 6.54x54 M384
6x55 6.55x55 V385
6x58 6.58x58 S388
TM7
7x30 7.31x30 P396
7x31 7.32x31 E397
7x34 7.35x34 W400
7x35 7.36x35 E401
7x38 7.39x38 Y404
7x41 7.42x41 C407
7x42 7.43x42 Y408