PDB
5VAI
Resolution
4.1 Å
Released
May 24, 2017
Receptor
GLP-1
Class
B1
Species
Oryctolagus cuniculus
Ligand
glucagon-like peptide 1-(7-37) (Human)
Function
Agonist
Reference
10.1038/NATURE22394

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Ligand Amino Acid Generic Number Segment Interaction Type
glucagon-like peptide 1-(7-37) (Human) L32 N-term polar (hydrogen bond with backbone)
glucagon-like peptide 1-(7-37) (Human) L32 N-term Van der Waals
glucagon-like peptide 1-(7-37) (Human) T35 N-term Van der Waals
glucagon-like peptide 1-(7-37) (Human) W39 N-term Van der Waals
glucagon-like peptide 1-(7-37) (Human) W39 N-term aromatic (face-to-edge)
glucagon-like peptide 1-(7-37) (Human) D68 N-term Van der Waals
glucagon-like peptide 1-(7-37) (Human) Y69 N-term hydrophobic
glucagon-like peptide 1-(7-37) (Human) Y69 N-term Van der Waals
glucagon-like peptide 1-(7-37) (Human) W91 N-term Van der Waals
glucagon-like peptide 1-(7-37) (Human) W91 N-term hydrophobic
glucagon-like peptide 1-(7-37) (Human) L118 N-term Van der Waals
glucagon-like peptide 1-(7-37) (Human) E128 N-term polar (charge-assisted hydrogen bond)
glucagon-like peptide 1-(7-37) (Human) E138 1.33x33 TM1 polar (charge-assisted hydrogen bond)
glucagon-like peptide 1-(7-37) (Human) E139 1.34x34 TM1 Van der Waals
glucagon-like peptide 1-(7-37) (Human) L142 1.37x37 TM1 Van der Waals
glucagon-like peptide 1-(7-37) (Human) L142 1.37x37 TM1 hydrophobic
glucagon-like peptide 1-(7-37) (Human) R190 2.60x60 TM2 Van der Waals
glucagon-like peptide 1-(7-37) (Human) V194 2.64x64 TM2 Van der Waals
glucagon-like peptide 1-(7-37) (Human) K197 2.67x67 TM2 polar (charge-assisted hydrogen bond)
glucagon-like peptide 1-(7-37) (Human) L201 2.71x71 TM2 Van der Waals
glucagon-like peptide 1-(7-37) (Human) L201 2.71x71 TM2 hydrophobic
glucagon-like peptide 1-(7-37) (Human) M204 2.74x74 TM2 polar (hydrogen bond)
glucagon-like peptide 1-(7-37) (Human) Y205 2.75x75 TM2 hydrophobic
glucagon-like peptide 1-(7-37) (Human) Q211 2.81x81 TM2 Van der Waals
glucagon-like peptide 1-(7-37) (Human) H212 ECL1 Van der Waals
glucagon-like peptide 1-(7-37) (Human) H212 ECL1 aromatic (edge-to-face)
glucagon-like peptide 1-(7-37) (Human) M233 3.36x36 TM3 Van der Waals
glucagon-like peptide 1-(7-37) (Human) M233 3.36x36 TM3 hydrophobic
glucagon-like peptide 1-(7-37) (Human) Q234 3.37x37 TM3 Van der Waals
glucagon-like peptide 1-(7-37) (Human) V237 3.40x40 TM3 Van der Waals
glucagon-like peptide 1-(7-37) (Human) Y241 3.44x44 TM3 Van der Waals
glucagon-like peptide 1-(7-37) (Human) W297 45.51x51 ECL2 Van der Waals
glucagon-like peptide 1-(7-37) (Human) W297 45.51x51 ECL2 polar (hydrogen bond with backbone)
glucagon-like peptide 1-(7-37) (Human) T298 45.52x52 ECL2 polar (hydrogen bond)
glucagon-like peptide 1-(7-37) (Human) T298 45.52x52 ECL2 polar (hydrogen bond)
glucagon-like peptide 1-(7-37) (Human) R299 ECL2 polar (charge-assisted hydrogen bond)
glucagon-like peptide 1-(7-37) (Human) R299 ECL2 polar (hydrogen bond with backbone)
glucagon-like peptide 1-(7-37) (Human) W306 5.36x37 TM5 polar (hydrogen bond)
glucagon-like peptide 1-(7-37) (Human) I309 5.39x39 TM5 Van der Waals
glucagon-like peptide 1-(7-37) (Human) I309 5.39x39 TM5 hydrophobic
glucagon-like peptide 1-(7-37) (Human) I313 5.43x43 TM5 hydrophobic
glucagon-like peptide 1-(7-37) (Human) F381 7.36x35 TM7 hydrophobic
glucagon-like peptide 1-(7-37) (Human) F385 7.40x39 TM7 hydrophobic
glucagon-like peptide 1-(7-37) (Human) F385 7.40x39 TM7 Van der Waals
glucagon-like peptide 1-(7-37) (Human) L388 7.43x42 TM7 Van der Waals
glucagon-like peptide 1-(7-37) (Human) L388 7.43x42 TM7 hydrophobic

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ICL1 R H L H ICL1ECL1 H Q W D G L L S Y Q D S ECL1ICL2 A V F ICL2ECL2 D E G C W T R N S ECL2ICL3 N L M C K T D I ICL3ECL3 V M D E H A R G T ECL3N-term M A G A P S P L R L A L L L L G A V G R A G P R P Q G A T V S L S E T V Q K W R E Y R R Q C Q H F L T E A P P L A T G L F C N R T F D D Y A C W P D G A P G S F V N V S C P W Y L P W A S N V L Q G H V Y R F C T T E G H W L H K D N S S L P W R D L S E C E E S R R G E K S S N-termC-term S M K P L K C P T S S L S S G A T G G S S V Y A A T S Q A C S C-term P E E Q L L S 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 T A A Q Q L G C R L V F L L M Q Y C V A A N Y Y W L L V E G A Y L Y T L L A F S E Q R I F K L Y L S I G W G V P L L F V I 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 I R V I C I V V S K L K A K C R L A K S T L T L I P L L G T H E V I F A F L R F V 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 V Q R V Q M E S W E R E H L R 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 S 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 K L Y L S G I W G V P L L F V I 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 6 I A V M L G Q F S T F S L E T F L K V 7

GPCRdb(A)
GPCRdb(B)
GLP-1 receptor
TM1
1x29 1.33x33 E138
1x30 1.34x34 E139
1x33 1.37x37 L142
TM2
2x53 2.60x60 R190
2x57 2.64x64 V194
2x60 2.67x67 K197
2x64 2.71x71 L201
2x67 2.74x74 M204
2x68 2.75x75 Y205
2x74 2.81x81 Q211
TM3
3x32 3.36x36 M233
3x33 3.37x37 Q234
3x36 3.40x40 V237
3x40 3.44x44 Y241
ECL2
45x51 45.51x51 W297
45x52 45.52x52 T298
TM5
5x41 5.36x37 W306
5x43 5.39x39 I309
5x47 5.43x43 I313
TM7
7x31 7.36x35 F381
7x35 7.40x39 F385
7x38 7.43x42 L388