PDB
5VBL
Resolution
2.6 Å
Released
May 31, 2017
Receptor
apelin
Class
A
Species
Homo sapiens
Ligand
Function
AMG3054
Agonist
Reference
10.1016/J.STR.2017.04.008

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
AMG3054 E20 N-term hydrophobic
AMG3054 Y21 N-term polar (hydrogen bond with backbone)
AMG3054 T22 N-term hydrophobic
AMG3054 D23 N-term polar (hydrogen bond)
AMG3054 D23 N-term polar (hydrogen bond with backbone)
AMG3054 W24 N-term hydrophobic
AMG3054 Y35 1.39x39 TM1 Van der Waals
AMG3054 W85 2.60x60 TM2 hydrophobic
AMG3054 W85 2.60x60 TM2 aromatic (edge-to-face)
AMG3054 W85 2.60x60 TM2 halogen contact
AMG3054 Y88 2.63x63 TM2 hydrophobic
AMG3054 T89 2.64x64 TM2 Van der Waals
AMG3054 R91 2.66x66 TM2 Van der Waals
AMG3054 Y93 ECL1 hydrophobic
AMG3054 F110 3.33x33 TM3 Van der Waals
AMG3054 R168 4.64x65 TM4 Van der Waals
AMG3054 R168 4.64x65 TM4 polar (charge-charge)
AMG3054 L173 ECL2 hydrophobic
AMG3054 E174 ECL2 hydrophobic
AMG3054 N175 ECL2 polar (hydrogen bond with backbone)
AMG3054 T176 ECL2 polar (hydrogen bond)
AMG3054 N177 ECL2 polar (hydrogen bond with backbone)
AMG3054 Y182 45.51x51 ECL2 Van der Waals
AMG3054 M183 45.52x52 ECL2 Van der Waals
AMG3054 Y185 ECL2 hydrophobic
AMG3054 E198 5.35x36 TM5 hydrophobic
AMG3054 Y264 6.51x51 TM6 polar (hydrogen bond)
AMG3054 V267 6.54x54 TM6 Van der Waals
AMG3054 K268 6.55x55 TM6 polar (charge-charge)
AMG3054 K268 6.55x55 TM6 Van der Waals
AMG3054 K268 6.55x55 TM6 polar (hydrogen bond)
AMG3054 Y271 6.58x58 TM6 hydrophobic
AMG3054 Y271 6.58x58 TM6 polar (hydrogen bond)
AMG3054 F291 7.35x34 TM7 hydrophobic
AMG3054 T295 7.39x38 TM7 hydrophobic
AMG3054 Y299 7.43x42 TM7 aromatic (edge-to-face)
AMG3054 Y299 7.43x42 TM7 hydrophobic

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

Download PDB file

Snake plot — Download: PNG | SVG
ICL1 S R E K R ICL1ECL1 Y D W P F ECL1ICL2 P V A N A R L R ICL2ECL2 T T G D L E N T T K V Q C Y M D Y S M V A T V S ECL2ICL3 R K E ICL3ECL3 L H W ECL3N-term M E E G G D F D N Y Y G A D N Q S E C E Y T D W K S S G N-termC-term Q S R C A G T S H S S S G E K S A S Y S S G H S Q G P G P N M G K G G E Q M H E K S I P Y S Q E T L V V D C-term A L I P A I Y M L V F L L G T T G N G L V L W T V F R S R S A D I F I A S L A V A D L T F V V T L P L W A T Y T Y R D G T F F C K L S S Y L I F V N M Y A S V F C L T G L S F D R Y L A I V R L R V S G A V A T A V L W V L A A L L A M P V M V L R S E W A W E V G L G V S S T T V G F V V P F T I M L T C Y F F I A Q T I A G H F R I E G L R K R R R L L S I I V V L V V T F A L C W M P Y H L V K T L Y M L G S L P C D F D L F L M N I F P Y C T C I S Y V N S C L N P F L Y A F F D P R C T S G F R Q A M L C C
Helix box plot — Download: PNG | SVG G N G T T G L L F V L M Y I A P I L A 1 A S L A V A D L T F V V T L P L W A T Y 2 G T L C F V S A Y M N V F I L Y S S L K 3 G A V A T A V L W V L A A L L A M P V 4 Y C T L M I T F P V V F G V T T S S V G L 5 V V L V V T F A L C W M P Y H L V K T L 6 F P N L C S N V Y S I C T C Y P F I N 7

GPCRdb(A)
GPCRdb(A)
apelin receptor
TM1
1x39 1.39x39 Y35
TM2
2x60 2.60x60 W85
2x63 2.63x63 Y88
2x64 2.64x64 T89
2x66 2.66x66 R91
TM3
3x33 3.33x33 F110
TM4
4x65 4.64x65 R168
ECL2
45x51 45.51x51 Y182
45x52 45.52x52 M183
TM5
5x36 5.35x36 E198
TM6
6x51 6.51x51 Y264
6x54 6.54x54 V267
6x55 6.55x55 K268
6x58 6.58x58 Y271
TM7
7x34 7.35x34 F291
7x38 7.39x38 T295
7x42 7.43x42 Y299