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

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Ligand Amino Acid Generic Number Segment Interaction Type
Peptide 5 S31 N-term Van der Waals
Peptide 5 L32 N-term hydrophobic
Peptide 5 W33 N-term polar (hydrogen bond with backbone)
Peptide 5 P137 N-term hydrophobic
Peptide 5 L141 1.36x36 TM1 hydrophobic
Peptide 5 L142 1.37x37 TM1 hydrophobic
Peptide 5 Y145 1.40x40 TM1 hydrophobic
Peptide 5 Y148 1.43x43 TM1 aromatic (edge-to-face)
Peptide 5 Y148 1.43x43 TM1 hydrophobic
Peptide 5 Y152 1.47x47 TM1 polar (hydrogen bond)
Peptide 5 R190 2.60x60 TM2 polar (hydrogen bond)
Peptide 5 V194 2.64x64 TM2 Van der Waals
Peptide 5 K197 2.67x67 TM2 hydrophobic
Peptide 5 D198 2.68x68 TM2 Van der Waals
Peptide 5 L201 2.71x71 TM2 hydrophobic
Peptide 5 K202 2.72x72 TM2 hydrophobic
Peptide 5 M204 2.74x74 TM2 hydrophobic
Peptide 5 Y205 2.75x75 TM2 polar (hydrogen bond)
Peptide 5 Y205 2.75x75 TM2 aromatic (edge-to-face)
Peptide 5 Y205 2.75x75 TM2 hydrophobic
Peptide 5 L217 ECL1 hydrophobic
Peptide 5 Q221 ECL1 hydrophobic
Peptide 5 F230 3.33x33 TM3 hydrophobic
Peptide 5 M233 3.36x36 TM3 hydrophobic
Peptide 5 Q234 3.37x37 TM3 Van der Waals
Peptide 5 V237 3.40x40 TM3 Van der Waals
Peptide 5 Y241 3.44x44 TM3 Van der Waals
Peptide 5 E294 ECL2 Van der Waals
Peptide 5 A295 ECL2 Van der Waals
Peptide 5 C296 45.50x50 ECL2 hydrophobic
Peptide 5 A298 45.52x52 ECL2 Van der Waals
Peptide 5 R299 ECL2 hydrophobic
Peptide 5 R299 ECL2 polar (hydrogen bond)
Peptide 5 N300 ECL2 polar (hydrogen bond with backbone)
Peptide 5 W306 5.36x37 TM5 hydrophobic
Peptide 5 I313 5.43x43 TM5 Van der Waals
Peptide 5 L314 5.44x44 TM5 Van der Waals
Peptide 5 V365 6.54x54 TM6 Van der Waals
Peptide 5 D372 ECL3 polar (hydrogen bond)
Peptide 5 R380 7.35x34 TM7 polar (charge-charge)
Peptide 5 R380 7.35x34 TM7 polar (hydrogen bond)
Peptide 5 K383 7.38x37 TM7 Van der Waals
Peptide 5 L384 7.39x38 TM7 hydrophobic
Peptide 5 E387 7.42x41 TM7 polar (hydrogen bond)
Peptide 5 L388 7.43x42 TM7 hydrophobic
Peptide 5 T391 7.46x45 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
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
TM3
3x29 3.33x33 F230
3x32 3.36x36 M233
3x33 3.37x37 Q234
3x36 3.40x40 V237
3x40 3.44x44 Y241
ECL2
45x50 45.50x50 C296
45x52 45.52x52 T298
TM5
5x41 5.36x37 W306
5x47 5.43x43 I313
5x48 5.44x44 L314
TM6
6x49 6.54x54 V365
TM7
7x30 7.35x34 R380
7x33 7.38x37 K383
7x34 7.39x38 L384
7x37 7.42x41 E387
7x38 7.43x42 L388
7x41 7.46x45 T391