Structure information

MRGPRD

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

9DQJ

SPECIES

Homo sapiens

RESOLUTION

2.900

PREFERRED CHAIN

A

REFERENCE

PUBLICATION DATE

Dec. 11, 2024

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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
EP-3945 Y106 3.33x33 TM3 hydrophobic
EP-3945 Y109 3.36x36 TM3 hydrophobic
EP-3945 C164 4.64x64 TM4 polar (hydrogen bond with backbone)
EP-3945 C164 4.64x64 TM4 Van der Waals
EP-3945 F170 ECL2 hydrophobic
EP-3945 D179 5.37x38 TM5 polar (charge-assisted hydrogen bond)
EP-3945 Q182 5.40x41 TM5 polar (hydrogen bond)
EP-3945 Q182 5.40x41 TM5 Van der Waals
EP-3945 A183 5.41x42 TM5 hydrophobic
EP-3945 A183 5.41x42 TM5 Van der Waals
EP-3945 S238 6.52x52 TM6 Van der Waals
EP-3945 W241 6.55x55 TM6 Van der Waals
EP-3945 W241 6.55x55 TM6 aromatic (face-to-face)
EP-3945 F242 6.56x56 TM6 hydrophobic
EP-3945 F242 6.56x56 TM6 Van der Waals
EP-3945 Y245 6.59x59 TM6 polar (hydrogen bond)

Ligands

EP-3945

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Residue Diagrams

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


GPCRdb(A)
GPCRdb(A)
MRGPRD
TM3
3x33 3.33x33 Y106
3x36 3.36x36 Y109
TM4
4x64 4.64x64 C164
TM5
5x38 5.37x38 D179
5x41 5.40x41 Q182
5x42 5.41x42 A183
TM6
6x52 6.52x52 S238
6x55 6.55x55 W241
6x56 6.56x56 F242
6x59 6.59x59 Y245