PDB
8YWF
Resolution
2.7 Å
Released
April 16, 2025
Receptor
GLP-1
Class
B1
Species
Homo sapiens
Ligand
retatrutide
Function
Agonist
Reference
—

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Ligand Amino Acid Generic Number Segment Interaction Type
retatrutide V30 N-term polar (hydrogen bond with backbone)
retatrutide V30 N-term Van der Waals
retatrutide S31 N-term Van der Waals
retatrutide S31 N-term polar (hydrogen bond with backbone)
retatrutide L32 N-term polar (hydrogen bond with backbone)
retatrutide L32 N-term Van der Waals
retatrutide T35 N-term Van der Waals
retatrutide V36 N-term Van der Waals
retatrutide V36 N-term hydrophobic
retatrutide W39 N-term Van der Waals
retatrutide W39 N-term aromatic (face-to-edge)
retatrutide E68 N-term Van der Waals
retatrutide Y88 N-term Van der Waals
retatrutide Y88 N-term hydrophobic
retatrutide W91 N-term hydrophobic
retatrutide R121 N-term Van der Waals
retatrutide L123 N-term Van der Waals
retatrutide L123 N-term hydrophobic
retatrutide E138 1.33x33 TM1 polar (charge-assisted hydrogen bond)
retatrutide L141 1.36x36 TM1 hydrophobic
retatrutide L141 1.36x36 TM1 Van der Waals
retatrutide Y148 1.43x43 TM1 hydrophobic
retatrutide Y148 1.43x43 TM1 Van der Waals
retatrutide V194 2.64x64 TM2 Van der Waals
retatrutide L201 2.71x71 TM2 hydrophobic
retatrutide L201 2.71x71 TM2 Van der Waals
retatrutide Y205 2.75x75 TM2 hydrophobic
retatrutide Y205 2.75x75 TM2 Van der Waals
retatrutide H212 ECL1 Van der Waals
retatrutide M233 3.36x36 TM3 Van der Waals
retatrutide Q234 3.37x37 TM3 Van der Waals
retatrutide Q234 3.37x37 TM3 polar (hydrogen bond)
retatrutide V237 3.40x40 TM3 Van der Waals
retatrutide V237 3.40x40 TM3 hydrophobic
retatrutide Y241 3.44x44 TM3 Van der Waals
retatrutide T298 45.52x52 ECL2 Van der Waals
retatrutide T298 45.52x52 ECL2 polar (hydrogen bond)
retatrutide R299 ECL2 polar (charge-assisted hydrogen bond)
retatrutide N300 ECL2 polar (hydrogen bond)
retatrutide N300 ECL2 Van der Waals
retatrutide N300 ECL2 polar (hydrogen bond with backbone)
retatrutide W306 5.36x37 TM5 Van der Waals
retatrutide W306 5.36x37 TM5 hydrophobic
retatrutide R310 5.40x40 TM5 polar (charge-assisted hydrogen bond)
retatrutide I313 5.43x43 TM5 hydrophobic
retatrutide I313 5.43x43 TM5 Van der Waals
retatrutide R380 ECL3 polar (charge-assisted hydrogen bond)
retatrutide L384 7.39x38 TM7 hydrophobic
retatrutide L384 7.39x38 TM7 Van der Waals
retatrutide E387 7.42x41 TM7 polar (charge-assisted hydrogen bond)
retatrutide L388 7.43x42 TM7 hydrophobic
retatrutide L388 7.43x42 TM7 Van der Waals

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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
1x39 1.43x43 Y148
TM2
2x57 2.64x64 V194
2x64 2.71x71 L201
2x68 2.75x75 Y205
TM3
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
5x44 5.40x40 R310
5x47 5.43x43 I313
TM7
7x34 7.39x38 L384
7x37 7.42x41 E387
7x38 7.43x42 L388