PDB
4NC3
Resolution
2.8 Å
Released
Dec. 18, 2013
Receptor
5-HT2B
Class
A
Species
Homo sapiens
Ligand
Function
ergotamine
Agonist
Reference
10.1126/SCIENCE.1244142

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Ligand Amino Acid Generic Number Segment Interaction Type
ergotamine W131 3.28x28 TM3 Van der Waals
ergotamine L132 3.29x29 TM3 hydrophobic
ergotamine D135 3.32x32 TM3 polar (hydrogen bond)
ergotamine D135 3.32x32 TM3 polar (charge-charge)
ergotamine V136 3.33x33 TM3 hydrophobic
ergotamine S139 3.36x36 TM3 Van der Waals
ergotamine T140 3.37x37 TM3 Van der Waals
ergotamine C207 45.50x50 ECL2 Van der Waals
ergotamine V208 45.51x51 ECL2 hydrophobic
ergotamine L209 45.52x52 ECL2 hydrophobic
ergotamine L209 45.52x52 ECL2 polar (hydrogen bond with backbone)
ergotamine T210 ECL2 Van der Waals
ergotamine K211 ECL2 hydrophobic
ergotamine F217 5.38x39 TM5 hydrophobic
ergotamine M218 5.39x40 TM5 hydrophobic
ergotamine G221 5.42x43 TM5 Van der Waals
ergotamine S222 5.43x44 TM5 Van der Waals
ergotamine A225 5.46x461 TM5 Van der Waals
ergotamine W337 6.48x48 TM6 Van der Waals
ergotamine F340 6.51x51 TM6 hydrophobic
ergotamine F340 6.51x51 TM6 aromatic (edge-to-face)
ergotamine F341 6.52x52 TM6 aromatic (edge-to-face)
ergotamine N344 6.55x55 TM6 Van der Waals
ergotamine L347 6.58x58 TM6 hydrophobic
ergotamine V348 6.59x59 TM6 Van der Waals
ergotamine Q359 7.32x31 TM7 Van der Waals
ergotamine L362 7.35x34 TM7 hydrophobic
ergotamine E363 7.36x35 TM7 hydrophobic
ergotamine V366 7.39x38 TM7 Van der Waals
ergotamine Y370 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
5-HT2B receptor
TM3
3x28 3.28x28 W131
3x29 3.29x29 L132
3x32 3.32x32 D135
3x33 3.33x33 V136
3x36 3.36x36 S139
3x37 3.37x37 T140
ECL2
45x50 45.50x50 C207
45x51 45.51x51 V208
45x52 45.52x52 L209
TM5
5x39 5.38x39 F217
5x40 5.39x40 M218
5x43 5.42x43 G221
5x44 5.43x44 S222
5x461 5.46x461 A225
TM6
6x48 6.48x48 W337
6x51 6.51x51 F340
6x52 6.52x52 F341
6x55 6.55x55 N344
6x58 6.58x58 L347
6x59 6.59x59 V348
TM7
7x31 7.32x31 Q359
7x34 7.35x34 L362
7x35 7.36x35 E363
7x38 7.39x38 V366
7x42 7.43x42 Y370