9WQB: 5-HT2B receptor

5-HT2B receptor bound to IHCH-6122 in complex with an antibody obtained by cryo-electron microscopy (cryoEM). Determined by electron microscopy at 3.18 Å resolution. Released 16 Sept 2026.

Method: Electron microscopy
Resolution: 3.18 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,047
Mol. weight: 85.74 kDa
Ligands: A1EYD
Released: 16 Sept 2026

Explore 9WQB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9WQB contains 29 α-helices and 45 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	55-81	27
α-helix	83-85	3
α-helix	88-102	15
α-helix	103-107	5
α-helix	108-116	9
α-helix	127-158	32
α-helix	169-187	19
α-helix	189-192	4
β-strand	196-197	2	1
α-helix	202-204	3
α-helix	217-221	5
α-helix	222	1
α-helix	223-227	5
α-helix	228-245	18
α-helix	320-349	30
α-helix	355-381	27
α-helix	385-389	5

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	2
β-strand	10-12	3	3
β-strand	19-25	7	2
β-strand	32-37	6	3
β-strand	44-48	5	3
β-strand	52-53	2	3
α-helix	54	1
β-strand	61-65	5	2
β-strand	69-74	6	2
α-helix	79-81	3
β-strand	84-89	6	3
α-helix	95	1
β-strand	96-97	2	3
β-strand	102-104	3	3
β-strand	110	1	4
β-strand	113-117	5	5
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	5
β-strand	139	1	4
β-strand	144-149	6	6
β-strand	152-153	2	6
β-strand	158-162	5	5
α-helix	163-166	4
β-strand	172-181	10	5
α-helix	182-187	6
β-strand	190-196	7	6
β-strand	204-209	6	6

Chain C: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-10	4
β-strand	11-12	2	8
β-strand	18-25	8	7
β-strand	34-39	6	9
β-strand	45-52	8	9
β-strand	57-60	4	9
α-helix	62-64	3
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-98	7	9
β-strand	101-104	4	1
β-strand	109-112	4	1
β-strand	116-117	2	9
β-strand	121-123	3	9
β-strand	124-125	2	8
α-helix	128-130	3
β-strand	136-138	3	10
β-strand	152-159	8	10
β-strand	165-168	4	11
β-strand	173	1	11
β-strand	177-179	3	10
β-strand	183-184	2	10
α-helix	185	1
β-strand	190-196	7	10
α-helix	200-203	4
β-strand	209-214	6	11
β-strand	219-224	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5-hydroxytryptamine receptor 2B	A	protein	318	Homo sapiens	P41595 (AlphaFold model)
Anti-5-HT2B Fab light chain	B	protein	213	Homo sapiens
Anti-5-HT2B Fab heavy chain	C	protein	247	Homo sapiens

Sequence of entity 1 (A), FASTA

>9WQB_1 5-hydroxytryptamine receptor 2B (chains A)
GPGSGSGTESIPEEMKQIVEEQGNKLHWAALLILMVIIPTIGGNTLVILAVSLEKKLQYA
TNYFLMSLAVADLLVGLFVMPIALLTIMFEAMWPLPLVLCPAWLFLDVLFSTASIWHLCA
ISVDRYIAIKKPIQANQYNSRATAFIKITVVWLISIGIAIPVPIKGIETDVDNPNNITCV
LTKERFGDFMLFGSLAAFFTPLAIMIVTYFLTIHALQKKRLLSGSRQTISNEQRASKVLG
IVFFLFLLMWCPFFITNITLVLCDSCNQTTLQMLLEIFVWIGYVSSGVNPLVYTLFNKTF
RDAFGRYITCNYRATKSV

Sequence of entity 2 (B), FASTA

>9WQB_2 Anti-5-HT2B Fab light chain (chains B)
DIVLIQSPAIMSASPGEKVTITCSASSSVSYMHWFQQKPGTSPKLWIYSTSNLASGVPAR
FSGSGSGTSYSLTISRMEAEDAATYYCQQRSSYPLTFGAGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSLPVTKSFNRGEC

Sequence of entity 3 (C), FASTA

>9WQB_3 Anti-5-HT2B Fab heavy chain (chains C)
EVQLQQSGPELVKPGASVKLSCKASGYTFTSSWMHWVKQRPGQGLEWIGNIYPSNGGTNY
NERFKSKATLTVDRSSNTAYMQLSSLTSEDSAVYFCARFGSFITTILTTYYNPVDYWGQG
TTLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCENLYFQSGSH
HHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1EYD	3-piperazin-1-yl-5,6,7,8-tetrahydroisoquinoline	C13 H19 N3	1

Primary citation

Structure-based design of subtype-selective psychedelic analogs. Li, H., Tang, L., Zhang, J. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-77658-y · PubMed

Other PDB entries of the same protein (UniProt P41595 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4IB4 2.7 Å, Crystal structure of the chimeric protein of 5-HT2B-BRIL in complex with ergotamine
7SRQ 2.7 Å, 5-HT2B receptor bound to LSD obtained by cryo-electron microscopy (cryoEM)
4NC3 2.8 Å, Crystal structure of the 5-HT2B receptor solved using serial femtosecond crystallography…
5TVN 2.9 Å, Crystal structure of the LSD-bound 5-HT2B receptor
7SRR 2.9 Å, 5-HT2B receptor bound to LSD in complex with heterotrimeric mini-Gq protein obtained by…
6DRY 2.92 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
9WNG 2.98 Å, 5HT2BR-fab heterotrimer in complex with a novel antagonist IHCH-2330
5TUD 3.0 Å, Structural Insights into the Extracellular Recognition of the Human Serotonin 2B…
6DRX 3.1 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
6DRZ 3.1 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
6DS0 3.19 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
9WQA 3.28 Å, 5-HT2B receptor bound to IHCH-1906 in complex with an antibody obtained by cryo-electron…

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