PDB
8YW3
Resolution
2.7 Å
Released
Sept. 18, 2024
Receptor
GLP-1
Class
B1
Species
Homo sapiens
Ligand
Function
retatrutide
Agonist
Reference
10.1038/S41421-024-00700-0

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Ligand Amino Acid Generic Number Segment Interaction Type
retatrutide V30 N-term Van der Waals
retatrutide S31 N-term Van der Waals
retatrutide L32 N-term hydrophobic
retatrutide T35 N-term hydrophobic
retatrutide T35 N-term polar (hydrogen bond)
retatrutide V36 N-term hydrophobic
retatrutide W39 N-term hydrophobic
retatrutide E68 N-term Van der Waals
retatrutide Y69 N-term hydrophobic
retatrutide Y88 N-term Van der Waals
retatrutide L89 N-term hydrophobic
retatrutide P90 N-term hydrophobic
retatrutide W91 N-term hydrophobic
retatrutide R121 N-term polar (hydrogen bond)
retatrutide L123 N-term hydrophobic
retatrutide P137 N-term Van der Waals
retatrutide E138 1.33x33 TM1 hydrophobic
retatrutide E138 1.33x33 TM1 polar (hydrogen bond)
retatrutide E138 1.33x33 TM1 polar (charge-charge)
retatrutide L141 1.36x36 TM1 hydrophobic
retatrutide L142 1.37x37 TM1 Van der Waals
retatrutide L144 1.39x39 TM1 hydrophobic
retatrutide Y145 1.40x40 TM1 hydrophobic
retatrutide Y148 1.43x43 TM1 aromatic (edge-to-face)
retatrutide Y148 1.43x43 TM1 hydrophobic
retatrutide Y152 1.47x47 TM1 Van der Waals
retatrutide V194 2.64x64 TM2 hydrophobic
retatrutide K197 2.67x67 TM2 hydrophobic
retatrutide K197 2.67x67 TM2 polar (hydrogen bond)
retatrutide L201 2.71x71 TM2 hydrophobic
retatrutide K202 2.72x72 TM2 Van der Waals
retatrutide Y205 2.75x75 TM2 polar (hydrogen bond)
retatrutide Y205 2.75x75 TM2 hydrophobic
retatrutide Q210 ECL1 Van der Waals
retatrutide W214 ECL1 hydrophobic
retatrutide W214 ECL1 aromatic (face-to-face)
retatrutide F230 3.33x33 TM3 hydrophobic
retatrutide M233 3.36x36 TM3 Van der Waals
retatrutide Q234 3.37x37 TM3 polar (hydrogen bond)
retatrutide V237 3.40x40 TM3 hydrophobic
retatrutide Y241 3.44x44 TM3 Van der Waals
retatrutide T298 45.52x52 ECL2 polar (hydrogen bond)
retatrutide R299 ECL2 polar (charge-charge)
retatrutide R299 ECL2 polar (hydrogen bond)
retatrutide N300 ECL2 polar (hydrogen bond with backbone)
retatrutide W306 5.36x37 TM5 hydrophobic
retatrutide I313 5.43x43 TM5 Van der Waals
retatrutide E364 6.53x53 TM6 polar (charge-charge)
retatrutide D372 ECL3 polar (hydrogen bond)
retatrutide R380 7.35x34 TM7 polar (charge-charge)
retatrutide L384 7.39x38 TM7 hydrophobic
retatrutide E387 7.42x41 TM7 polar (charge-charge)
retatrutide E387 7.42x41 TM7 hydrophobic
retatrutide L388 7.43x42 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(B)
GLP-1 receptor
TM1
1x29 1.33x33 E138
1x32 1.36x36 L141
1x33 1.37x37 L142
1x35 1.39x39 L144
1x36 1.40x40 Y145
1x39 1.43x43 Y148
1x43 1.47x47 Y152
TM2
2x57 2.64x64 V194
2x60 2.67x67 K197
2x64 2.71x71 L201
2x65 2.72x72 K202
2x68 2.75x75 Y205
TM3
3x29 3.33x33 F230
3x32 3.36x36 M233
3x33 3.37x37 Q234
3x36 3.40x40 V237
3x40 3.44x44 Y241
ECL2
45x52 45.52x52 T298
TM5
5x41 5.36x37 W306
5x47 5.43x43 I313
TM6
6x48 6.53x53 E364
TM7
7x30 7.35x34 R380
7x34 7.39x38 L384
7x37 7.42x41 E387
7x38 7.43x42 L388