8BHA | pdb_00008bha

GABA-A receptor a5 homomer - a5V3 - Basmisanil - HR

PDB DOI: https://doi.org/10.2210/pdb8BHA/pdb
EM Map EMD-16050: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2022-10-30 Released: 2023-11-01
Deposition Author(s): Malinauskas, T.M., Wahid, A.A., Hardwick, S.W., Chirgadze, D.Y., Miller, P.S.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.67 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The molecular basis of drug selectivity for alpha 5 subunit-containing GABA A receptors.

Kasaragod, V.B., Malinauskas, T., Wahid, A.A., Lengyel, J., Knoflach, F., Hardwick, S.W., Jones, C.F., Chen, W.N., Lucas, X., El Omari, K., Chirgadze, D.Y., Aricescu, A.R., Cecere, G., Hernandez, M.C., Miller, P.S.

(2023) Nat Struct Mol Biol 30: 1936-1946

PubMed: 37903907 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-023-01133-1
Primary Citation Related Structures:
8BEJ, 8BGI, 8BHA, 8BHB, 8BHG, 8BHI, 8BHK, 8BHM, 8BHO, 8BHQ, 8BHR, 8BHS

PubMed Abstract:
α5 subunit-containing γ-aminobutyric acid type A (GABA _A) receptors represent a promising drug target for neurological and neuropsychiatric disorders. Altered expression and function contributes to neurodevelopmental disorders such as Dup15q and Angelman syndromes, developmental epilepsy and autism. Effective drug action without side effects is dependent on both α5-subtype selectivity and the strength of the positive or negative allosteric modulation (PAM or NAM). Here we solve structures of drugs bound to the α5 subunit. These define the molecular basis of binding and α5 selectivity of the β-carboline, methyl 6,7-dimethoxy-4-ethyl-β-carboline-3-carboxylate (DMCM), type II benzodiazepine NAMs, and a series of isoxazole NAMs and PAMs. For the isoxazole series, each molecule appears as an 'upper' and 'lower' moiety in the pocket. Structural data and radioligand binding data reveal a positional displacement of the upper moiety containing the isoxazole between the NAMs and PAMs. Using a hybrid molecule we directly measure the functional contribution of the upper moiety to NAM versus PAM activity. Overall, these structures provide a framework by which to understand distinct modulator binding modes and their basis of α5-subtype selectivity, appreciate structure-activity relationships, and empower future structure-based drug design campaigns.

Organizational Affiliation

Department of Pharmacology, University of Cambridge, Cambridge, UK.

Macromolecule Content

Total Structure Weight: 208.62 kDa
Atom Count: 13,805
Modeled Residue Count: 1,680
Deposited Residue Count: 1,800
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit alpha-5	A, B, C, D, E	360	Homo sapiens	Mutation(s): 21 Gene Names: GABRA5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P31644 (Homo sapiens) Explore P31644 Go to UniProtKB: P31644
PHAROS: P31644 GTEx: ENSG00000186297
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31644
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E	Go to GlyGen: P31644-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QI0 (Subject of Investigation/LOI) Query on QI0 Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E]	Basmisanil C₂₁ H₂₀ F N₃ O₅ S VCGRFBXVSFAGGA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain N [auth E] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain N [auth E] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D], N [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E]