6WH4 | pdb_00006wh4

Crystal structure of HTR2A with inverse agonist

PDB DOI: https://doi.org/10.2210/pdb6WH4/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Escherichia coli
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2020-04-07 Released: 2020-09-23
Deposition Author(s): Kim, K.L., Che, T., Krumm, B.E., Roth, B.L.
Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.304 (Depositor), 0.290 (DCC)
R-Value Work:
0.258 (Depositor), 0.260 (DCC)
R-Value Observed:
0.260 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of a Hallucinogen-Activated Gq-Coupled 5-HT 2A Serotonin Receptor

Kim, K.L., Che, T., Panova, O., DiBerto, J.F., Lyu, J., Krumm, B.E., Wacker, D., Robertson, M.J., Seven, A.B., Nichols, D.E., Shoichet, B.K., Skiniotis, G., Roth, B.L.

(2020) Cell 182: 1574-1588

DOI: https://doi.org/10.1016/j.cell.2020.08.024

Macromolecule Content

Total Structure Weight: 155.44 kDa
Atom Count: 8,108
Modelled Residue Count: 1,111
Deposited Residue Count: 1,344
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 fusion	A, B, C	448	Homo sapiens, Escherichia coli	Mutation(s): 0 Gene Names: HTR2A, HTR2, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P28223 (Homo sapiens) Explore P28223 Go to UniProtKB: P28223
PHAROS: P28223 GTEx: ENSG00000102468
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P28223P0ABE7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain M [auth C]	G [auth A], M [auth C]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain G [auth A] Focus chain M [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth C]
89F (Subject of Investigation/LOI) Query on 89F Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] SDF format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain L [auth C]	D [auth A], I [auth B], L [auth C]	1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine C₂₀ H₂₄ N₂ S₂ RLJFTICUTYVZDG-SFHVURJKSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain L [auth C]
OLA Query on OLA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain Q [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth C]	E [auth A], F [auth A], K [auth B], Q [auth C]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
NDS Query on NDS Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	ETHYL DIMETHYL AMMONIO PROPANE SULFONATE C₇ H₁₇ N O₃ S NNCRHRDBFDCWPA-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain H [auth A] SDF format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain H [auth A] mmCIF format, chain O [auth C]	H [auth A], J [auth B], N [auth C], O [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
89F	BindingDB: 6WH4	Ki: min: 0.1, max: 3.16 (nM) from 4 assay(s)
89F	BindingDB: 6WH4	IC50: min: 6.3, max: 56 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.304 (Depositor), 0.290 (DCC)
R-Value Work: 0.258 (Depositor), 0.260 (DCC)
R-Value Observed: 0.260 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.38	α = 90
b = 177.31	β = 90
c = 280.59	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	R37 DA045657
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	RO1 MH112205

Revision History (Full details and data files)

Version 1.0: 2020-09-23
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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Help and Resources

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Crystal structure of HTR2A with inverse agonist

Structure of a Hallucinogen-Activated Gq-Coupled 5-HT 2A Serotonin Receptor

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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