PDB
9IVM
Resolution
3.2 Å
Released
Nov. 13, 2024
Receptor
GLP-1
Class
B1
Species
Homo sapiens
Ligands
glucagon-like peptide 1-(9-36)
LSN3318839
Function
Agonist (partial)
PAM
Reference
—
glucagon-like peptide 1-(9-36) LSN3318839

NGL is a WebGL based 3D viewer powered by MMTF.

Download PDB file
Download list in excel
Ligand Amino Acid Generic Number Segment Interaction Type
glucagon-like peptide 1-(9-36) S31 N-term Van der Waals
glucagon-like peptide 1-(9-36) S31 N-term polar (hydrogen bond)
glucagon-like peptide 1-(9-36) L32 N-term polar (hydrogen bond with backbone)
glucagon-like peptide 1-(9-36) L32 N-term Van der Waals
glucagon-like peptide 1-(9-36) V36 N-term hydrophobic
glucagon-like peptide 1-(9-36) V36 N-term Van der Waals
glucagon-like peptide 1-(9-36) W39 N-term Van der Waals
glucagon-like peptide 1-(9-36) W39 N-term aromatic (face-to-edge)
glucagon-like peptide 1-(9-36) E68 N-term polar (charge-assisted hydrogen bond)
glucagon-like peptide 1-(9-36) Y88 N-term Van der Waals
glucagon-like peptide 1-(9-36) Y88 N-term hydrophobic
glucagon-like peptide 1-(9-36) L89 N-term Van der Waals
glucagon-like peptide 1-(9-36) P90 N-term Van der Waals
glucagon-like peptide 1-(9-36) P90 N-term hydrophobic
glucagon-like peptide 1-(9-36) W91 N-term Van der Waals
glucagon-like peptide 1-(9-36) W91 N-term hydrophobic
glucagon-like peptide 1-(9-36) R121 N-term polar (charge-assisted hydrogen bond)
glucagon-like peptide 1-(9-36) L123 N-term Van der Waals
glucagon-like peptide 1-(9-36) L123 N-term hydrophobic
LSN3318839 E138 1.33x33 TM1 Van der Waals
glucagon-like peptide 1-(9-36) E138 1.33x33 TM1 Van der Waals
LSN3318839 E138 1.33x33 TM1 polar (hydrogen bond with backbone)
LSN3318839 L141 1.36x36 TM1 hydrophobic
LSN3318839 L141 1.36x36 TM1 Van der Waals
glucagon-like peptide 1-(9-36) L141 1.36x36 TM1 hydrophobic
glucagon-like peptide 1-(9-36) L141 1.36x36 TM1 Van der Waals
LSN3318839 L142 1.37x37 TM1 Van der Waals
LSN3318839 L142 1.37x37 TM1 hydrophobic
glucagon-like peptide 1-(9-36) L144 1.39x39 TM1 hydrophobic
LSN3318839 Y145 1.40x40 TM1 Van der Waals
LSN3318839 Y145 1.40x40 TM1 aromatic (face-to-face)
LSN3318839 I146 1.41x41 TM1 Van der Waals
LSN3318839 I146 1.41x41 TM1 hydrophobic
glucagon-like peptide 1-(9-36) Y148 1.43x43 TM1 Van der Waals
glucagon-like peptide 1-(9-36) Y148 1.43x43 TM1 aromatic (edge-to-face)
glucagon-like peptide 1-(9-36) V194 2.64x64 TM2 hydrophobic
glucagon-like peptide 1-(9-36) V194 2.64x64 TM2 Van der Waals
glucagon-like peptide 1-(9-36) K197 2.67x67 TM2 polar (charge-assisted hydrogen bond)
LSN3318839 D198 2.68x68 TM2 polar (hydrogen bond with backbone)
LSN3318839 D198 2.68x68 TM2 polar (charge-assisted hydrogen bond)
glucagon-like peptide 1-(9-36) L201 2.71x71 TM2 Van der Waals
LSN3318839 L201 2.71x71 TM2 hydrophobic
LSN3318839 L201 2.71x71 TM2 Van der Waals
glucagon-like peptide 1-(9-36) L201 2.71x71 TM2 hydrophobic
LSN3318839 K202 2.72x72 TM2 polar (charge-assisted hydrogen bond)
glucagon-like peptide 1-(9-36) Y205 2.75x75 TM2 Van der Waals
glucagon-like peptide 1-(9-36) Y205 2.75x75 TM2 polar (hydrogen bond)
glucagon-like peptide 1-(9-36) Q210 ECL1 polar (hydrogen bond)
glucagon-like peptide 1-(9-36) Q210 ECL1 Van der Waals
glucagon-like peptide 1-(9-36) W214 ECL1 aromatic (face-to-edge)
glucagon-like peptide 1-(9-36) W214 ECL1 Van der Waals
glucagon-like peptide 1-(9-36) Q221 ECL1 Van der Waals
glucagon-like peptide 1-(9-36) F230 3.33x33 TM3 hydrophobic
glucagon-like peptide 1-(9-36) M233 3.36x36 TM3 polar (hydrogen bond)
glucagon-like peptide 1-(9-36) T298 45.52x52 ECL2 Van der Waals
glucagon-like peptide 1-(9-36) R299 ECL2 polar (charge-assisted hydrogen bond)
glucagon-like peptide 1-(9-36) N300 ECL2 polar (hydrogen bond)
glucagon-like peptide 1-(9-36) N300 ECL2 Van der Waals
glucagon-like peptide 1-(9-36) W306 5.36x37 TM5 Van der Waals
glucagon-like peptide 1-(9-36) W306 5.36x37 TM5 hydrophobic
glucagon-like peptide 1-(9-36) R380 7.35x34 TM7 polar (charge-assisted hydrogen bond)
glucagon-like peptide 1-(9-36) L384 7.39x38 TM7 hydrophobic
glucagon-like peptide 1-(9-36) L384 7.39x38 TM7 Van der Waals
glucagon-like peptide 1-(9-36) L388 7.43x42 TM7 Van der Waals
glucagon-like peptide 1-(9-36) L388 7.43x42 TM7 hydrophobic

NGL is a WebGL based 3D viewer powered by MMTF.

Download PDB file

NGL is a WebGL based 3D viewer powered by MMTF.

Download PDB file

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
1x29 1.33x33 E138
1x32 1.36x36 L141
1x33 1.37x37 L142
1x35 1.39x39 L144
1x36 1.40x40 Y145
1x37 1.41x41 I146
1x39 1.43x43 Y148
TM2
2x57 2.64x64 V194
2x60 2.67x67 K197
2x61 2.68x68 D198
2x64 2.71x71 L201
2x65 2.72x72 K202
2x68 2.75x75 Y205
TM3
3x29 3.33x33 F230
3x32 3.36x36 M233
ECL2
45x52 45.52x52 T298
TM5
5x41 5.36x37 W306
TM7
7x30 7.35x34 R380
7x34 7.39x38 L384
7x38 7.43x42 L388