PDB
7F54
Resolution
3.0 Å
Released
Nov. 3, 2021
Receptor
MC4
Class
A
Species
Homo sapiens
Ligands
Function
afamelanotide
Agonist
Calcium
PAM
Reference
10.1038/S41422-021-00552-3
afamelanotide Calcium

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Ligand Amino Acid Generic Number Segment Interaction Type
afamelanotide Q43 N-term Van der Waals
afamelanotide F51 1.39x39 TM1 Van der Waals
Calcium E100 2.60x60 TM2 metal coordination
afamelanotide E100 2.60x60 TM2 hydrophobic
afamelanotide T101 2.61x61 TM2 Van der Waals
afamelanotide V103 2.63x63 TM2 Van der Waals
afamelanotide I104 2.64x64 TM2 hydrophobic
afamelanotide V119 3.22x22 TM3 Van der Waals
Calcium D122 3.25x25 TM3 polar (charge-charge)
afamelanotide D122 3.25x25 TM3 Van der Waals
Calcium D122 3.25x25 TM3 metal coordination
afamelanotide I125 3.28x28 TM3 Van der Waals
Calcium D126 3.29x29 TM3 metal coordination
afamelanotide D126 3.29x29 TM3 polar (charge-charge)
afamelanotide I129 3.32x32 TM3 hydrophobic
afamelanotide L133 3.36x36 TM3 hydrophobic
afamelanotide F184 4.60x60 TM4 Van der Waals
afamelanotide I185 4.61x61 TM4 Van der Waals
afamelanotide S188 4.64x64 TM4 polar (hydrogen bond with backbone)
afamelanotide V193 5.39x39 TM5 hydrophobic
afamelanotide I194 5.40x40 TM5 hydrophobic
afamelanotide L197 5.43x43 TM5 hydrophobic
afamelanotide F261 6.51x51 TM6 hydrophobic
afamelanotide H264 6.54x54 TM6 polar (hydrogen bond)
afamelanotide L265 6.55x55 TM6 hydrophobic
afamelanotide Y268 6.58x58 TM6 aromatic (edge-to-face)
afamelanotide Y268 6.58x58 TM6 hydrophobic
afamelanotide Y268 6.58x58 TM6 polar (hydrogen bond)
afamelanotide P272 ECL3 hydrophobic
afamelanotide M281 ECL3 hydrophobic
afamelanotide F284 7.35x34 TM7 Van der Waals
afamelanotide N285 7.36x35 TM7 Van der Waals
afamelanotide L288 7.39x38 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
MC4 receptor
TM1
1x39 1.39x39 F51
TM2
2x60 2.60x60 E100
2x61 2.61x61 T101
2x63 2.63x63 V103
2x64 2.64x64 I104
TM3
3x22 3.22x22 V119
3x25 3.25x25 D122
3x28 3.28x28 I125
3x29 3.29x29 D126
3x32 3.32x32 I129
3x36 3.36x36 L133
TM4
4x60 4.60x60 F184
4x61 4.61x61 I185
4x64 4.64x64 S188
TM5
5x39 5.39x39 V193
5x40 5.40x40 I194
5x43 5.43x43 L197
TM6
6x51 6.51x51 F261
6x54 6.54x54 H264
6x55 6.55x55 L265
6x58 6.58x58 Y268
TM7
7x34 7.35x34 F284
7x35 7.36x35 N285
7x38 7.39x38 L288