8BGI | pdb_00008bgi

GABA-A receptor a5 homomer - a5V1 - Flumazenil

PDB DOI: https://doi.org/10.2210/pdb8BGI/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-10-27 Released: 2023-11-08
Deposition Author(s): Miller, P.S., Malinauskas, T.M., Omari, K.E., Aricescu, A.R.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.277 (Depositor), 0.285 (DCC)
R-Value Work:
0.254 (Depositor), 0.263 (DCC)
R-Value Observed:
0.255 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 213.25 kDa
Atom Count: 14,002
Modeled Residue Count: 1,675
Deposited Residue Count: 1,805
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit alpha-5	A, B, C, D, E	361	Homo sapiens	Mutation(s): 1 Gene Names: GABRA5
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P9N Query on P9N Download:Ideal Coordinates CCD File SDF format, chain WA [auth E] SDF format, chain W [auth B] SDF format, chain NA [auth D] SDF format, chain M [auth A] SDF format, chain FA [auth C] MOL2 format, chain WA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain FA [auth C] mmCIF format, chain WA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain FA [auth C]	FA [auth C], M [auth A], NA [auth D], W [auth B], WA [auth E]	Pregnanolone C₂₁ H₃₄ O₂ AURFZBICLPNKBZ-YZRLXODZSA-N		Interactions Focus chain FA [auth C] Focus chain M [auth A] Focus chain NA [auth D] Focus chain W [auth B] Focus chain WA [auth E] Interactions & Density Focus chain FA [auth C] Focus chain M [auth A] Focus chain NA [auth D] Focus chain W [auth B] Focus chain WA [auth E]
FYP (Subject of Investigation/LOI) Query on FYP Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain PA [auth E] SDF format, chain MA [auth D] SDF format, chain L [auth A] SDF format, chain EA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain MA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain EA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain MA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain EA [auth C]	EA [auth C], L [auth A], MA [auth D], PA [auth E], V [auth B]	ethyl 8-fluoro-5-methyl-6-oxo-5,6-dihydro-4H-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate C₁₅ H₁₄ F N₃ O₃ OFBIFZUFASYYRE-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain L [auth A] Focus chain MA [auth D] Focus chain PA [auth E] Focus chain V [auth B] Interactions & Density Focus chain EA [auth C] Focus chain L [auth A] Focus chain MA [auth D] Focus chain PA [auth E] Focus chain V [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain XA [auth E] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain OA [auth D] SDF format, chain GA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain GA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain XA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain GA [auth C]	GA [auth C] N [auth A] OA [auth D] X [auth B] XA [auth E] GA [auth C], N [auth A], OA [auth D], X [auth B], XA [auth E], Y [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain GA [auth C] Focus chain N [auth A] Focus chain OA [auth D] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Interactions & Density Focus chain GA [auth C] Focus chain N [auth A] Focus chain OA [auth D] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain HA [auth D] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain Q [auth B] SDF format, chain QA [auth E] SDF format, chain R [auth B] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain Z [auth C] SDF format, chain VA [auth E] SDF format, chain UA [auth E] SDF format, chain U [auth B] SDF format, chain TA [auth E] SDF format, chain T [auth B] SDF format, chain SA [auth E] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain LA [auth D] SDF format, chain J [auth A] SDF format, chain IA [auth D] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain VA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain VA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain LA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] F [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], F [auth A], G [auth A], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], LA [auth D], O [auth B], P [auth B], Q [auth B], QA [auth E], R [auth B], RA [auth E], S [auth B], SA [auth E], T [auth B], TA [auth E], U [auth B], UA [auth E], VA [auth E], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain Z [auth C]