Structure information

5-HT1A receptor

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

8PKM

SPECIES

Homo sapiens

RESOLUTION

2.900

PREFERRED CHAIN

R

REFERENCE

PUBLICATION DATE

May 29, 2024

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Ligand Interaction Browser

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Ligand Amino Acid Generic Number Segment Interaction Type
Ligand Amino Acid Generic Number Segment Interaction Type
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate R134 3.50x50 TM3 Van der Waals
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate K345 6.35x35 TM6 polar (charge-assisted hydrogen bond)
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate T346 6.36x36 TM6 polar (hydrogen bond)
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate T346 6.36x36 TM6 Van der Waals
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate I399 7.52x52 TM7 Van der Waals
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate Y400 7.53x53 TM7 polar (hydrogen bond with backbone)
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate Y400 7.53x53 TM7 Van der Waals
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate F403 7.56x56 TM7 polar (hydrogen bond with backbone)
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate F403 7.56x56 TM7 Van der Waals
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate N404 8.47x47 H8 polar (hydrogen bond)
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate N404 8.47x47 H8 Van der Waals
(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate K405 8.48x48 H8 Van der Waals

Ligands

(2r)-1-(Heptadecanoyloxy)-3-{[(R)-Hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-Tetrahydroxy-4-(Phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-Yl (5z,8z,11z,14z)-Icosa-5,8,11,14-Tetraenoate

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Residue Diagrams

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
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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
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Residue Table


GPCRdb(A)
GPCRdb(A)
5-HT1A receptor
TM3
3x50 3.50x50 R134
TM6
6x35 6.35x35 K345
6x36 6.36x36 T346
TM7
7x52 7.52x52 I399
7x53 7.53x53 Y400
7x56 7.56x56 F403
H8
8x47 8.47x47 N404
8x48 8.48x48 K405