PDB
8E3Y
Resolution
2.3 Å
Released
Nov. 23, 2022
Receptor
VPAC1
Class
B1
Species
Homo sapiens
Ligand
PACAP-27 (Human)
Function
Agonist
Reference
10.1038/S41467-022-34629-3

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Ligand Amino Acid Generic Number Segment Interaction Type
PACAP-27 (Human) V40 N-term hydrophobic
PACAP-27 (Human) I89 N-term hydrophobic
PACAP-27 (Human) F90 N-term hydrophobic
PACAP-27 (Human) F93 N-term hydrophobic
PACAP-27 (Human) G123 N-term polar (hydrogen bond with backbone)
PACAP-27 (Human) G123 N-term Van der Waals
PACAP-27 (Human) L124 N-term hydrophobic
PACAP-27 (Human) L124 N-term Van der Waals
PACAP-27 (Human) K127 N-term polar (charge-assisted hydrogen bond)
PACAP-27 (Human) D132 1.29x29 TM1 Van der Waals
PACAP-27 (Human) D132 1.29x29 TM1 polar (hydrogen bond with backbone)
PACAP-27 (Human) Q135 1.32x32 TM1 Van der Waals
PACAP-27 (Human) T136 1.33x33 TM1 polar (hydrogen bond)
PACAP-27 (Human) T136 1.33x33 TM1 Van der Waals
PACAP-27 (Human) Y139 1.36x36 TM1 Van der Waals
PACAP-27 (Human) Y139 1.36x36 TM1 hydrophobic
PACAP-27 (Human) V142 1.39x39 TM1 hydrophobic
PACAP-27 (Human) V142 1.39x39 TM1 Van der Waals
PACAP-27 (Human) Y146 1.43x43 TM1 Van der Waals
PACAP-27 (Human) Y146 1.43x43 TM1 aromatic (edge-to-face)
PACAP-27 (Human) Y150 1.47x47 TM1 Van der Waals
PACAP-27 (Human) Y150 1.47x47 TM1 polar (hydrogen bond)
PACAP-27 (Human) R188 2.60x60 TM2 polar (charge-assisted hydrogen bond)
PACAP-27 (Human) K195 2.67x67 TM2 polar (charge-assisted hydrogen bond)
PACAP-27 (Human) F200 2.72x72 TM2 aromatic (face-to-edge)
PACAP-27 (Human) F200 2.72x72 TM2 polar (hydrogen bond with backbone)
PACAP-27 (Human) F200 2.72x72 TM2 Van der Waals
PACAP-27 (Human) E204 ECL1 Van der Waals
PACAP-27 (Human) C208 ECL1 Van der Waals
PACAP-27 (Human) F222 3.36x36 TM3 aromatic (face-to-edge)
PACAP-27 (Human) F222 3.36x36 TM3 Van der Waals
PACAP-27 (Human) Q223 3.37x37 TM3 polar (hydrogen bond)
PACAP-27 (Human) V226 3.40x40 TM3 Van der Waals
PACAP-27 (Human) V226 3.40x40 TM3 hydrophobic
PACAP-27 (Human) D287 45.52x52 ECL2 polar (charge-assisted hydrogen bond)
PACAP-27 (Human) T288 ECL2 Van der Waals
PACAP-27 (Human) I289 ECL2 polar (hydrogen bond with backbone)
PACAP-27 (Human) I289 ECL2 Van der Waals
PACAP-27 (Human) N290 ECL2 polar (hydrogen bond)
PACAP-27 (Human) W294 5.36x37 TM5 Van der Waals
PACAP-27 (Human) W294 5.36x37 TM5 hydrophobic
PACAP-27 (Human) I297 5.39x39 TM5 Van der Waals
PACAP-27 (Human) D362 ECL3 Van der Waals
PACAP-27 (Human) K369 7.38x37 TM7 Van der Waals
PACAP-27 (Human) M370 7.39x38 TM7 Van der Waals
PACAP-27 (Human) E373 7.42x41 TM7 polar (charge-assisted hydrogen bond)
PACAP-27 (Human) L374 7.43x42 TM7 Van der Waals
PACAP-27 (Human) L374 7.43x42 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(B)
VPAC1 receptor
TM1
1x25 1.29x29 D132
1x28 1.32x32 Q135
1x29 1.33x33 T136
1x32 1.36x36 Y139
1x35 1.39x39 V142
1x39 1.43x43 Y146
1x43 1.47x47 Y150
TM2
2x53 2.60x60 R188
2x60 2.67x67 K195
TM3
3x32 3.36x36 F222
3x33 3.37x37 Q223
3x36 3.40x40 V226
ECL2
45x52 45.52x52 D287
TM5
5x41 5.36x37 W294
5x43 5.39x39 I297
TM7
7x33 7.38x37 K369
7x34 7.39x38 M370
7x37 7.42x41 E373
7x38 7.43x42 L374