Structure information

M1 receptor

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

6ZG9

SPECIES

Homo sapiens

RESOLUTION

2.500

PREFERRED CHAIN

A

REFERENCE

10.1016/J.CELL.2021.11.001

PUBLICATION DATE

Oct. 6, 2021

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Ligand Interaction Browser

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Ligand Amino Acid Generic Number Segment Interaction Type
Ligand Amino Acid Generic Number Segment Interaction Type
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one L81 2.60x59 TM2 hydrophobic
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one Y82 2.61x60 TM2 hydrophobic
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one Y85 2.64x63 TM2 hydrophobic
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one L102 3.29x29 TM3 hydrophobic
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one D105 3.32x32 TM3 polar (charge-assisted hydrogen bond)
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one S109 3.36x36 TM3 Van der Waals
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one C178 45.50x50 ECL2 polar (hydrogen bond with backbone)
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one C178 45.50x50 ECL2 Van der Waals
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one Y179 45.51x51 ECL2 Van der Waals
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one W378 6.48x48 TM6 hydrophobic
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one W378 6.48x48 TM6 Van der Waals
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one Y381 6.51x51 TM6 Van der Waals
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one Y404 7.39x38 TM7 hydrophobic
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one Y404 7.39x38 TM7 Van der Waals
7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one Y408 7.43x42 TM7 Van der Waals

Ligands

7-fluoro-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1H-benzimidazol-2-one

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Residue Diagrams

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
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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
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Residue Table


GPCRdb(A)
GPCRdb(A)
M1 receptor
TM2
2x59 2.60x59 L81
2x60 2.61x60 Y82
2x63 2.64x63 Y85
TM3
3x29 3.29x29 L102
3x32 3.32x32 D105
3x36 3.36x36 S109
ECL2
45x50 45.50x50 C178
45x51 45.51x51 Y179
TM6
6x48 6.48x48 W378
6x51 6.51x51 Y381
TM7
7x38 7.39x38 Y404
7x42 7.43x42 Y408