PDB
7F4H
Resolution
2.7 Å
Released
Sept. 8, 2021
Receptor
MC1
Class
A
Species
Homo sapiens
Ligands
Function
afamelanotide
Agonist
Calcium
PAM
Reference
10.1038/S41422-021-00557-Y
afamelanotide Calcium

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Ligand Amino Acid Generic Number Segment Interaction Type
afamelanotide D42 1.36x36 TM1 polar (charge-charge)
afamelanotide D42 1.36x36 TM1 polar (hydrogen bond)
afamelanotide F45 1.39x39 TM1 aromatic (face-to-face)
afamelanotide F45 1.39x39 TM1 aromatic (pi-cation)
afamelanotide N91 2.57x57 TM2 Van der Waals
Calcium E94 2.60x60 TM2 metal coordination
afamelanotide E94 2.60x60 TM2 polar (hydrogen bond)
afamelanotide E94 2.60x60 TM2 polar (charge-charge)
afamelanotide T95 2.61x61 TM2 Van der Waals
afamelanotide V97 2.63x63 TM2 hydrophobic
afamelanotide I98 2.64x64 TM2 hydrophobic
afamelanotide L113 3.21x21 TM3 Van der Waals
afamelanotide D117 3.25x25 TM3 polar (hydrogen bond)
Calcium D117 3.25x25 TM3 metal coordination
afamelanotide D117 3.25x25 TM3 polar (charge-charge)
afamelanotide D117 3.25x25 TM3 hydrophobic
Calcium D117 3.25x25 TM3 polar (charge-charge)
afamelanotide I120 3.28x28 TM3 Van der Waals
Calcium D121 3.29x29 TM3 metal coordination
afamelanotide D121 3.29x29 TM3 polar (hydrogen bond)
afamelanotide D121 3.29x29 TM3 polar (charge-charge)
afamelanotide D121 3.29x29 TM3 hydrophobic
afamelanotide T124 3.32x32 TM3 hydrophobic
afamelanotide C125 3.33x33 TM3 hydrophobic
afamelanotide M128 3.36x36 TM3 hydrophobic
afamelanotide I180 4.61x61 TM4 hydrophobic
afamelanotide Y183 ECL2 aromatic (pi-cation)
afamelanotide Y183 ECL2 polar (hydrogen bond with backbone)
afamelanotide V188 5.39x39 TM5 hydrophobic
afamelanotide L189 5.40x40 TM5 hydrophobic
afamelanotide L192 5.43x43 TM5 Van der Waals
afamelanotide F257 6.51x51 TM6 hydrophobic
afamelanotide H260 6.54x54 TM6 polar (hydrogen bond)
afamelanotide L261 6.55x55 TM6 hydrophobic
afamelanotide I264 6.58x58 TM6 hydrophobic
afamelanotide C267 6.61x61 TM6 Van der Waals
afamelanotide P268 ECL3 hydrophobic
afamelanotide F277 ECL3 hydrophobic
afamelanotide F280 7.35x34 TM7 Van der Waals
afamelanotide N281 7.36x35 TM7 Van der Waals
afamelanotide L284 7.39x38 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
MC1 receptor
TM1
1x36 1.36x36 D42
1x39 1.39x39 F45
TM2
2x57 2.57x57 N91
2x60 2.60x60 E94
2x61 2.61x61 T95
2x63 2.63x63 V97
2x64 2.64x64 I98
TM3
3x21 3.21x21 L113
3x25 3.25x25 D117
3x28 3.28x28 I120
3x29 3.29x29 D121
3x32 3.32x32 T124
3x33 3.33x33 C125
3x36 3.36x36 M128
TM4
4x61 4.61x61 I180
TM5
5x39 5.39x39 V188
5x40 5.40x40 L189
5x43 5.43x43 L192
TM6
6x51 6.51x51 F257
6x54 6.54x54 H260
6x55 6.55x55 L261
6x58 6.58x58 I264
6x61 6.61x61 C267
TM7
7x34 7.35x34 F280
7x35 7.36x35 N281
7x38 7.39x38 L284