PDB
9DYD
Resolution
3.0 Å
Released
Aug. 13, 2025
Receptor
5-HT1A
Class
A
Species
Homo sapiens
Ligands
(3aS,12bR)-asenapine
PtdIns4P
Function
Agonist (partial)
PAM
Reference
—
(3aS,12bR)-asenapine PtdIns4P

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Ligand Amino Acid Generic Number Segment Interaction Type
(3aS,12bR)-asenapine D116 3.32x32 TM3 polar (charge-assisted hydrogen bond)
(3aS,12bR)-asenapine V117 3.33x33 TM3 hydrophobic
(3aS,12bR)-asenapine V117 3.33x33 TM3 Van der Waals
(3aS,12bR)-asenapine C120 3.36x36 TM3 hydrophobic
(3aS,12bR)-asenapine C120 3.36x36 TM3 Van der Waals
(3aS,12bR)-asenapine T121 3.37x37 TM3 Van der Waals
(3aS,12bR)-asenapine I124 3.40x40 TM3 hydrophobic
(3aS,12bR)-asenapine I124 3.40x40 TM3 Van der Waals
PtdIns4P R134 3.50x50 TM3 polar (charge-assisted hydrogen bond)
(3aS,12bR)-asenapine I189 45.52x52 ECL2 Van der Waals
(3aS,12bR)-asenapine I189 45.52x52 ECL2 hydrophobic
(3aS,12bR)-asenapine S199 5.42x43 TM5 Van der Waals
(3aS,12bR)-asenapine T200 5.43x44 TM5 Van der Waals
(3aS,12bR)-asenapine A203 5.46x461 TM5 hydrophobic
(3aS,12bR)-asenapine A203 5.46x461 TM5 Van der Waals
PtdIns4P T346 6.36x36 TM6 Van der Waals
PtdIns4P I349 6.39x39 TM6 Van der Waals
PtdIns4P I349 6.39x39 TM6 hydrophobic
(3aS,12bR)-asenapine W358 6.48x48 TM6 Van der Waals
(3aS,12bR)-asenapine W358 6.48x48 TM6 aromatic (face-to-edge)
(3aS,12bR)-asenapine F361 6.51x51 TM6 hydrophobic
(3aS,12bR)-asenapine F361 6.51x51 TM6 Van der Waals
(3aS,12bR)-asenapine F362 6.52x52 TM6 aromatic (edge-to-face)
(3aS,12bR)-asenapine F362 6.52x52 TM6 Van der Waals
(3aS,12bR)-asenapine Y390 7.43x42 TM7 Van der Waals
PtdIns4P V398 7.51x51 TM7 Van der Waals
PtdIns4P V398 7.51x51 TM7 hydrophobic
PtdIns4P I399 7.52x52 TM7 polar (hydrogen bond with backbone)
PtdIns4P I399 7.52x52 TM7 Van der Waals
PtdIns4P Y400 7.53x53 TM7 Van der Waals
PtdIns4P Y402 7.55x55 TM7 hydrophobic
PtdIns4P Y402 7.55x55 TM7 Van der Waals
PtdIns4P F403 7.56x56 TM7 polar (hydrogen bond with backbone)
PtdIns4P F403 7.56x56 TM7 Van der Waals
PtdIns4P N404 8.47x47 H8 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
5-HT1A receptor
TM3
3x32 3.32x32 D116
3x33 3.33x33 V117
3x36 3.36x36 C120
3x37 3.37x37 T121
3x40 3.40x40 I124
3x50 3.50x50 R134
ECL2
45x52 45.52x52 I189
TM5
5x43 5.42x43 S199
5x44 5.43x44 T200
5x461 5.46x461 A203
TM6
6x36 6.36x36 T346
6x39 6.39x39 I349
6x48 6.48x48 W358
6x51 6.51x51 F361
6x52 6.52x52 F362
TM7
7x42 7.43x42 Y390
7x51 7.51x51 V398
7x52 7.52x52 I399
7x53 7.53x53 Y400
7x55 7.55x55 Y402
7x56 7.56x56 F403
H8
8x47 8.47x47 N404