Structure information

Rhodopsin

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

6FKD

SPECIES

Bos taurus

RESOLUTION

2.490

PREFERRED CHAIN

A

REFERENCE

10.1073/PNAS.1718084115

PUBLICATION DATE

April 4, 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
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one L125 3.40x40 TM3 hydrophobic
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one Y191 ECL2 hydrophobic
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one M207 5.42x43 TM5 hydrophobic
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one F208 5.43x44 TM5 hydrophobic
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one H211 5.46x461 TM5 Van der Waals
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one H211 5.46x461 TM5 polar (hydrogen bond with backbone)
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one F212 5.47x47 TM5 hydrophobic
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one F212 5.47x47 TM5 Van der Waals
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one F261 6.44x44 TM6 Van der Waals
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one F261 6.44x44 TM6 hydrophobic
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one C264 6.47x47 TM6 Van der Waals
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one W265 6.48x48 TM6 Van der Waals
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one W265 6.48x48 TM6 hydrophobic
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one Y268 6.51x51 TM6 hydrophobic
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one Y268 6.51x51 TM6 Van der Waals
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one A272 6.55x55 TM6 hydrophobic
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one A272 6.55x55 TM6 Van der Waals
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one M288 ECL3 Van der Waals
5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one M288 ECL3 hydrophobic

Ligands

5-chloro-2-(2-oxo-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-ylethyl)-3H-pyridin-6-one

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Residue Diagrams

F N I P F G L M I L L F M Y A A L M S F 1 L N L A V A D L F M V G F G F T T T L Y T 2 V V L S W L A I E G G L T A F F G E L N 3 A I M G V A F T W V M A L A C A A P P L 4 Y C F F I V I L P I I F H V V F M Y I V F 5 I I M V I A F L I C W L P Y A G V A F Y 6 V P N Y V A S T K A F F A P I T M F I 7
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ICL1 K K L R ICL1ECL1 Y F V F ECL1ICL2 P M S N F R F ICL2ECL2 W S R Y I P E G M Q C S C G I D Y Y T P H E E T ECL2ICL3 Q E ICL3ECL3 Q G S D F ECL3N-term M N G T E G P N F Y V P F S N K T G V V R S P F E A P Q Y Y L A N-termC-term C G K N P L G D D E A S T T V S K T E T S Q V A P A C-term E P W Q F S M L A A Y M F L L I M L G F P I N F L T L Y V T V Q H T P L N Y I L L N L A V A D L F M V F G G F T T T L Y T S L H G G P T G C N L E G F F A T L G G E I A L W S L V V L A I E R Y V V V C K G E N H A I M G V A F T W V M A L A C A A P P L V G N N E S F V I Y M F V V H F I I P L I V I F F C Y G Q L V F T V K E A A A Q Q S A T T Q K A E K E V T R M V I I M V I A F L I C W L P Y A G V A F Y I F T H G P I F M T I P A F F A K T S A V Y N P V I Y I M M N K Q M V T F R N C T L C
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Residue Table


GPCRdb(A)
GPCRdb(A)
Rhodopsin
TM3
3x40 3.40x40 L125
TM5
5x43 5.42x43 M207
5x44 5.43x44 F208
5x461 5.46x461 H211
5x47 5.47x47 F212
TM6
6x44 6.44x44 F261
6x47 6.47x47 C264
6x48 6.48x48 W265
6x51 6.51x51 Y268
6x55 6.55x55 A272