PDB
5NX2
Resolution
3.7 Å
Released
June 14, 2017
Receptor
GLP-1
Class
B1
Species
Homo sapiens
Ligand
Peptide 5
Function
Agonist
Reference
10.1038/NATURE22800

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Ligand Amino Acid Generic Number Segment Interaction Type
Peptide 5 L32 N-term Van der Waals
Peptide 5 L32 N-term polar (hydrogen bond with backbone)
Peptide 5 W33 N-term polar (hydrogen bond with backbone)
Peptide 5 W33 N-term Van der Waals
Peptide 5 P137 N-term hydrophobic
Peptide 5 P137 N-term Van der Waals
Peptide 5 L141 1.36x36 TM1 Van der Waals
Peptide 5 L141 1.36x36 TM1 hydrophobic
Peptide 5 L142 1.37x37 TM1 Van der Waals
Peptide 5 L142 1.37x37 TM1 hydrophobic
Peptide 5 Y145 1.40x40 TM1 Van der Waals
Peptide 5 Y145 1.40x40 TM1 hydrophobic
Peptide 5 Y148 1.43x43 TM1 hydrophobic
Peptide 5 Y148 1.43x43 TM1 Van der Waals
Peptide 5 Y152 1.47x47 TM1 polar (hydrogen bond)
Peptide 5 R190 2.60x60 TM2 polar (charge-assisted hydrogen bond)
Peptide 5 V194 2.64x64 TM2 Van der Waals
Peptide 5 K197 2.67x67 TM2 Van der Waals
Peptide 5 D198 2.68x68 TM2 Van der Waals
Peptide 5 L201 2.71x71 TM2 hydrophobic
Peptide 5 L201 2.71x71 TM2 Van der Waals
Peptide 5 K202 2.72x72 TM2 Van der Waals
Peptide 5 M204 2.74x74 TM2 Van der Waals
Peptide 5 Y205 2.75x75 TM2 polar (hydrogen bond)
Peptide 5 Y205 2.75x75 TM2 polar (hydrogen bond)
Peptide 5 L217 ECL1 Van der Waals
Peptide 5 L217 ECL1 hydrophobic
Peptide 5 Q221 ECL1 Van der Waals
Peptide 5 A295 ECL2 Van der Waals
Peptide 5 A295 ECL2 hydrophobic
Peptide 5 C296 45.50x50 ECL2 hydrophobic
Peptide 5 C296 45.50x50 ECL2 Van der Waals
Peptide 5 A298 45.52x52 ECL2 Van der Waals
Peptide 5 R299 ECL2 polar (charge-assisted hydrogen bond)
Peptide 5 N300 ECL2 polar (hydrogen bond)
Peptide 5 N300 ECL2 polar (hydrogen bond with backbone)
Peptide 5 N300 ECL2 Van der Waals
Peptide 5 W306 5.36x37 TM5 Van der Waals
Peptide 5 W306 5.36x37 TM5 hydrophobic
Peptide 5 I313 5.43x43 TM5 Van der Waals
Peptide 5 D372 ECL3 polar (charge-assisted hydrogen bond)
Peptide 5 R380 7.35x34 TM7 polar (charge-assisted hydrogen bond)
Peptide 5 L384 7.39x38 TM7 hydrophobic
Peptide 5 L384 7.39x38 TM7 Van der Waals
Peptide 5 E387 7.42x41 TM7 polar (charge-assisted hydrogen bond)
Peptide 5 L388 7.43x42 TM7 hydrophobic
Peptide 5 L388 7.43x42 TM7 Van der Waals

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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
1x32 1.36x36 L141
1x33 1.37x37 L142
1x36 1.40x40 Y145
1x39 1.43x43 Y148
1x43 1.47x47 Y152
TM2
2x53 2.60x60 R190
2x57 2.64x64 V194
2x60 2.67x67 K197
2x61 2.68x68 D198
2x64 2.71x71 L201
2x65 2.72x72 K202
2x67 2.74x74 M204
2x68 2.75x75 Y205
ECL2
45x50 45.50x50 C296
45x52 45.52x52 T298
TM5
5x41 5.36x37 W306
5x47 5.43x43 I313
TM7
7x30 7.35x34 R380
7x34 7.39x38 L384
7x37 7.42x41 E387
7x38 7.43x42 L388