PDB
9HB3
Resolution
2.5 Å
Released
June 4, 2025
Receptor
V2
Class
A
Species
Homo sapiens
Ligand
Mambaquaretin-1 K39A
Function
Inverse agonist
Reference
10.1038/S41467-025-59114-5

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Ligand Amino Acid Generic Number Segment Interaction Type
Mambaquaretin-1 K39A Q96 2.61x60 TM2 polar (hydrogen bond)
Mambaquaretin-1 K39A Q96 2.61x60 TM2 polar (hydrogen bond)
Mambaquaretin-1 K39A W99 2.64x63 TM2 Van der Waals
Mambaquaretin-1 K39A W99 2.64x63 TM2 hydrophobic
Mambaquaretin-1 K39A D103 ECL1 Van der Waals
Mambaquaretin-1 K39A D103 ECL1 polar (hydrogen bond with backbone)
Mambaquaretin-1 K39A R104 23.49x49 ECL1 Van der Waals
Mambaquaretin-1 K39A K116 3.29x29 TM3 polar (charge-assisted hydrogen bond)
Mambaquaretin-1 K39A Q119 3.32x32 TM3 polar (hydrogen bond)
Mambaquaretin-1 K39A F178 ECL2 aromatic (face-to-edge)
Mambaquaretin-1 K39A F178 ECL2 Van der Waals
Mambaquaretin-1 K39A T190 ECL2 Van der Waals
Mambaquaretin-1 K39A D191 ECL2 Van der Waals
Mambaquaretin-1 K39A W193 45.51x51 ECL2 aromatic (edge-to-face)
Mambaquaretin-1 K39A W193 45.51x51 ECL2 Van der Waals
Mambaquaretin-1 K39A A194 45.52x52 ECL2 Van der Waals
Mambaquaretin-1 K39A A194 45.52x52 ECL2 polar (hydrogen bond with backbone)
Mambaquaretin-1 K39A C195 ECL2 Van der Waals
Mambaquaretin-1 K39A R202 5.35x36 TM5 polar (charge-assisted hydrogen bond)
Mambaquaretin-1 K39A V206 5.39x40 TM5 Van der Waals
Mambaquaretin-1 K39A I209 5.42x43 TM5 hydrophobic
Mambaquaretin-1 K39A I209 5.42x43 TM5 Van der Waals
Mambaquaretin-1 K39A Q291 6.55x55 TM6 polar (hydrogen bond)
Mambaquaretin-1 K39A A294 6.58x58 TM6 Van der Waals
Mambaquaretin-1 K39A A294 6.58x58 TM6 hydrophobic
Mambaquaretin-1 K39A P298 ECL3 hydrophobic
Mambaquaretin-1 K39A P298 ECL3 Van der Waals
Mambaquaretin-1 K39A P306 ECL3 Van der Waals
Mambaquaretin-1 K39A P306 ECL3 polar (hydrogen bond with backbone)
Mambaquaretin-1 K39A F307 7.35x34 TM7 Van der Waals
Mambaquaretin-1 K39A F307 7.35x34 TM7 aromatic (face-to-edge)
Mambaquaretin-1 K39A F307 7.35x34 TM7 polar (hydrogen bond with backbone)
Mambaquaretin-1 K39A V308 7.36x35 TM7 Van der Waals
Mambaquaretin-1 K39A V308 7.36x35 TM7 hydrophobic
Mambaquaretin-1 K39A M311 7.39x38 TM7 Van der Waals
Mambaquaretin-1 K39A M311 7.39x38 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
V2 receptor
TM2
2x60 2.61x60 Q96
2x63 2.64x63 W99
ECL1
23x49 23.49x49 R104
TM3
3x29 3.29x29 K116
3x32 3.32x32 Q119
ECL2
45x51 45.51x51 W193
45x52 45.52x52 A194
TM5
5x36 5.35x36 R202
5x40 5.39x40 V206
5x43 5.42x43 I209
TM6
6x55 6.55x55 Q291
6x58 6.58x58 A294
TM7
7x34 7.35x34 F307
7x35 7.36x35 V308
7x38 7.39x38 M311