Structure information

5-HT2B receptor

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

6DRY

SPECIES

Homo sapiens

RESOLUTION

2.920

PREFERRED CHAIN

A

REFERENCE

10.1038/s41594-018-0116-7

PUBLICATION DATE

Aug. 29, 2018

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Ligand Interaction Browser

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Ligand Amino Acid Generic Number Segment Interaction Type
Ligand Amino Acid Generic Number Segment Interaction Type
methylergonovine D135 3.32x32 TM3 polar (charge-assisted hydrogen bond)
methylergonovine V136 3.33x33 TM3 hydrophobic
methylergonovine V136 3.33x33 TM3 Van der Waals
methylergonovine S139 3.36x36 TM3 Van der Waals
methylergonovine T140 3.37x37 TM3 polar (hydrogen bond)
methylergonovine V208 45.51x51 ECL2 Van der Waals
methylergonovine V208 45.51x51 ECL2 hydrophobic
methylergonovine L209 45.52x52 ECL2 polar (hydrogen bond with backbone)
methylergonovine L209 45.52x52 ECL2 Van der Waals
methylergonovine F217 5.38x39 TM5 hydrophobic
methylergonovine F217 5.38x39 TM5 Van der Waals
methylergonovine G221 5.42x43 TM5 Van der Waals
methylergonovine S222 5.43x44 TM5 Van der Waals
methylergonovine F340 6.51x51 TM6 hydrophobic
methylergonovine F340 6.51x51 TM6 Van der Waals
methylergonovine F341 6.52x52 TM6 aromatic (edge-to-face)
methylergonovine F341 6.52x52 TM6 Van der Waals
methylergonovine Q359 7.32x31 TM7 Van der Waals
methylergonovine L362 7.35x34 TM7 Van der Waals
methylergonovine E363 7.36x35 TM7 Van der Waals
methylergonovine V366 7.39x38 TM7 hydrophobic
methylergonovine V366 7.39x38 TM7 Van der Waals
methylergonovine Y370 7.43x42 TM7 Van der Waals

Ligands

methylergonovine

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Residue Diagrams

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
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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
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Residue Table


GPCRdb(A)
GPCRdb(A)
5-HT2B receptor
TM3
3x32 3.32x32 D135
3x33 3.33x33 V136
3x36 3.36x36 S139
3x37 3.37x37 T140
ECL2
45x51 45.51x51 V208
45x52 45.52x52 L209
TM5
5x39 5.38x39 F217
5x43 5.42x43 G221
5x44 5.43x44 S222
TM6
6x51 6.51x51 F340
6x52 6.52x52 F341
TM7
7x31 7.32x31 Q359
7x34 7.35x34 L362
7x35 7.36x35 E363
7x38 7.39x38 V366
7x42 7.43x42 Y370