9MUM: GluN1/GluN2A ligand-binding domain

Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 11, Glycine and Glutamate. Determined by X-ray diffraction at 1.97 Å resolution. Released 5 Mar 2025.

Method: X-ray diffraction
Resolution: 1.97 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,583
Mol. weight: 69.37 kDa
Ligands: GLY, GLU, A1BRB
Released: 5 Mar 2025

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

Secondary structure: helices and β-sheets

9MUM contains 34 α-helices and 40 β-strands across 2 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: 18 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	398-402	5	1
β-strand	405	1	2
β-strand	409	1	2
β-strand	410-413	4	1
α-helix	414-415	2
α-helix	419-422	4
β-strand	424	1	3
α-helix	429	1
β-strand	430	1	3
α-helix	431-432	2
β-strand	434-439	6	1
β-strand	450-456	7	1
α-helix	458-470	13
β-strand	474-478	5	1
β-strand	487	1	4
β-strand	498	1	4
α-helix	500-507	8
β-strand	512-513	2	1
β-strand	518	1	5
α-helix	521-524	4
β-strand	528-529	2	1
α-helix	530	1
α-helix	532	1
β-strand	534-543	10	5
α-helix	670-673	4
β-strand	681-682	2	5
β-strand	684	1	6
α-helix	688-695	8
α-helix	697-699	3
α-helix	700-706	7
β-strand	711	1	6
α-helix	714-722	9
β-strand	728-732	5	5
α-helix	733-742	10
β-strand	746-748	3	5
β-strand	754-758	5	5
β-strand	761-762	2	1
α-helix	769-781	13
α-helix	784-788	5
α-helix	789-793	5

Chain B: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	405-410	6	7
β-strand	413	1	8
β-strand	417	1	8
β-strand	418-420	3	7
β-strand	434-441	8	7
β-strand	449-457	9	7
α-helix	459-467	9
α-helix	468-472	5
β-strand	474-479	6	7
β-strand	488-489	2	9
β-strand	492-493	2	9
α-helix	495-501	7
β-strand	507-508	2	7
β-strand	513	1	10
α-helix	516-519	4
β-strand	522-524	3	7
β-strand	529-538	10	10
α-helix	668-671	4
α-helix	673-675	3
α-helix	679-680	2
β-strand	682-683	2	10
α-helix	689-697	9
α-helix	699-705	7
α-helix	706-708	3
α-helix	713-721	9
β-strand	727-731	5	10
α-helix	732-740	9
α-helix	743-745	3
β-strand	747-749	3	10
α-helix	750-753	4
β-strand	756-761	6	10
β-strand	764-766	3	7
α-helix	772-784	13
α-helix	787-796	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A	protein	306	Homo sapiens	Q05586 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2A	B	protein	297	Homo sapiens	Q12879 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9MUM_1 Glutamate receptor ionotropic, NMDA 1 (chains A)
MHHHHHHENLYFQGSMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTG
PNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEW
NGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRN
PSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSA
VLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVR
YQECDS

Sequence of entity 2 (B), FASTA

>9MUM_2 Glutamate receptor ionotropic, NMDA 2A (chains B)
MHHHHHHENLYFQGPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNST
NEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAV
MAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTV
PNGSTERNIRNNYPYMHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGC
KLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHN

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	1
GLU	Glutamic acid	C5 H9 N O4	1
A1BRB	5-[2-(3-chlorophenyl)-2,2-difluoroethoxy]-N-[1-(pyrazin-2-yl)cyclopropyl]pyrazi…	C20 H16 Cl F2 N5 O2	1

Primary citation

Design, Synthesis, and Characterization of GluN2A Negative Allosteric Modulators Suitable for In Vivo Exploration. Bischoff, F.P., Van Brandt, S., Viellevoye, M. et al. J Med Chem (2025) 68:4672-4693. DOI 10.1021/acs.jmedchem.4c02751 · PubMed

Other PDB entries of the same protein (UniProt Q05586 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GJ1 1.62 Å, NMDA bound to compound 339
5H8F 1.81 Å, Structure of the apo human GluN1/GluN2A LBD
9GIC 1.82 Å, NMDA bound to compound 345
3BYA 1.85 Å, Structure of a Calmodulin Complex
5H8Q 1.9 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE8324
9GIF 1.9 Å, NMDA bound to compound 288
9GIB 1.95 Å, NMDA bound to compound 380
9GID 2.0 Å, NMDA bound to compound 338
5KCJ 2.09 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE6901
9GIG 2.09 Å, NMDA bound to compound 387
5I2N 2.12 Å, Structure of the human GluN1/GluN2A LBD in complex with…
5H8H 2.23 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE3419

Browse structure collections

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