PDB
9C0K
Resolution
2.7 Å
Released
June 11, 2025
Receptor
GLP-1
Class
B1
Species
Homo sapiens
Ligand
Exendin-phe1
Function
Agonist
Reference
—

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Ligand Amino Acid Generic Number Segment Interaction Type
Exendin-phe1 T29 N-term polar (hydrogen bond)
Exendin-phe1 T29 N-term polar (hydrogen bond with backbone)
Exendin-phe1 T29 N-term Van der Waals
Exendin-phe1 V30 N-term Van der Waals
Exendin-phe1 V30 N-term polar (hydrogen bond with backbone)
Exendin-phe1 S31 N-term Van der Waals
Exendin-phe1 L32 N-term Van der Waals
Exendin-phe1 L32 N-term polar (hydrogen bond with backbone)
Exendin-phe1 V36 N-term Van der Waals
Exendin-phe1 V36 N-term hydrophobic
Exendin-phe1 W39 N-term hydrophobic
Exendin-phe1 W39 N-term Van der Waals
Exendin-phe1 E68 N-term Van der Waals
Exendin-phe1 Y69 N-term hydrophobic
Exendin-phe1 Y69 N-term Van der Waals
Exendin-phe1 Y88 N-term hydrophobic
Exendin-phe1 Y88 N-term Van der Waals
Exendin-phe1 W91 N-term hydrophobic
Exendin-phe1 W91 N-term Van der Waals
Exendin-phe1 R121 N-term polar (charge-assisted hydrogen bond)
Exendin-phe1 L123 N-term hydrophobic
Exendin-phe1 L123 N-term Van der Waals
Exendin-phe1 E138 1.33x33 TM1 polar (charge-assisted hydrogen bond)
Exendin-phe1 L141 1.36x36 TM1 hydrophobic
Exendin-phe1 L141 1.36x36 TM1 Van der Waals
Exendin-phe1 Y145 1.40x40 TM1 Van der Waals
Exendin-phe1 Y148 1.43x43 TM1 aromatic (face-to-edge)
Exendin-phe1 Y148 1.43x43 TM1 Van der Waals
Exendin-phe1 R190 2.60x60 TM2 Van der Waals
Exendin-phe1 L201 2.71x71 TM2 hydrophobic
Exendin-phe1 L201 2.71x71 TM2 Van der Waals
Exendin-phe1 Y205 2.75x75 TM2 Van der Waals
Exendin-phe1 W214 ECL1 hydrophobic
Exendin-phe1 W214 ECL1 Van der Waals
Exendin-phe1 M233 3.36x36 TM3 Van der Waals
Exendin-phe1 Y241 3.44x44 TM3 polar (hydrogen bond)
Exendin-phe1 Y241 3.44x44 TM3 Van der Waals
Exendin-phe1 T298 45.52x52 ECL2 Van der Waals
Exendin-phe1 I313 5.43x43 TM5 hydrophobic
Exendin-phe1 E364 6.53x53 TM6 Van der Waals
Exendin-phe1 L384 7.39x38 TM7 Van der Waals
Exendin-phe1 E387 7.42x41 TM7 polar (charge-assisted hydrogen bond)
Exendin-phe1 L388 7.43x42 TM7 Van der Waals
Exendin-phe1 L388 7.43x42 TM7 hydrophobic

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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
1x36 1.40x40 Y145
1x39 1.43x43 Y148
TM2
2x53 2.60x60 R190
2x64 2.71x71 L201
2x68 2.75x75 Y205
TM3
3x32 3.36x36 M233
3x40 3.44x44 Y241
ECL2
45x52 45.52x52 T298
TM5
5x47 5.43x43 I313
TM6
6x48 6.53x53 E364
TM7
7x34 7.39x38 L384
7x37 7.42x41 E387
7x38 7.43x42 L388