6WH4 | pdb_00006wh4

Crystal structure of HTR2A with inverse agonist


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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 89FClick on this verticalbar to view details

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 fusion
A, B, C
448Homo sapiensEscherichia coliMutation(s): 0 
Gene Names: HTR2AHTR2cybC
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP28223P0ABE7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth A],
M [auth C]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
89F (Subject of Investigation/LOI)
Query on 89F

Download Ideal Coordinates CCD File 
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
OLA
Query on OLA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
K [auth B],
Q [auth C]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
R [auth C]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
NDS
Query on NDS

Download Ideal Coordinates CCD File 
P [auth C]ETHYL DIMETHYL AMMONIO PROPANE SULFONATE
C7 H17 N O3 S
NNCRHRDBFDCWPA-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
N [auth C],
O [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
89F BindingDB:  6WH4 Ki: min: 0.1, max: 3.16 (nM) from 4 assay(s)
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 = 82.38α = 90
b = 177.31β = 90
c = 280.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 89FClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR37 DA045657
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesRO1 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