Structure of the human GluN1/GluN2A LBD in complex with N-ethyl-7-{[2-fluoro-3-(trifluoromethyl)phenyl]methyl}-2-methyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide (compound 29). Determined by X-ray diffraction at 2.12 Å resolution. Released 16 Mar 2016.
Explore 5I2N in 3D Show helices and sheets RCSB PDB PDBe
5I2N contains 32 α-helices and 39 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 7-12 | 6 | 1 |
| β-strand | 15 | 1 | 2 |
| β-strand | 19 | 1 | 2 |
| β-strand | 20-23 | 4 | 1 |
| α-helix | 24-25 | 2 | |
| β-strand | 36-43 | 8 | 1 |
| β-strand | 51-59 | 9 | 1 |
| α-helix | 61-72 | 12 | |
| β-strand | 76-81 | 6 | 1 |
| β-strand | 90-91 | 2 | 3 |
| β-strand | 94-95 | 2 | 3 |
| α-helix | 97-103 | 7 | |
| β-strand | 109-110 | 2 | 1 |
| β-strand | 115 | 1 | 4 |
| α-helix | 118-121 | 4 | |
| β-strand | 125-126 | 2 | 1 |
| α-helix | 127-129 | 3 | |
| β-strand | 131-140 | 10 | 4 |
| α-helix | 151-154 | 4 | |
| α-helix | 156-158 | 3 | |
| α-helix | 162-163 | 2 | |
| β-strand | 165-166 | 2 | 4 |
| α-helix | 172-180 | 9 | |
| α-helix | 182-188 | 7 | |
| α-helix | 189-191 | 3 | |
| α-helix | 196-204 | 9 | |
| β-strand | 210-214 | 5 | 4 |
| α-helix | 215-224 | 10 | |
| α-helix | 226-228 | 3 | |
| β-strand | 230-232 | 3 | 4 |
| β-strand | 239-244 | 6 | 4 |
| β-strand | 247-248 | 2 | 1 |
| α-helix | 255-267 | 13 | |
| α-helix | 270-278 | 9 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 6 | 1 | |
| β-strand | 7-11 | 5 | 5 |
| β-strand | 14 | 1 | 6 |
| β-strand | 18 | 1 | 6 |
| β-strand | 19-21 | 3 | 5 |
| β-strand | 33 | 1 | 7 |
| α-helix | 38 | 1 | |
| β-strand | 39 | 1 | 7 |
| α-helix | 40-41 | 2 | |
| β-strand | 43-48 | 6 | 5 |
| β-strand | 59-65 | 7 | 5 |
| α-helix | 67-79 | 13 | |
| β-strand | 83-87 | 5 | 5 |
| β-strand | 96-98 | 3 | 8 |
| β-strand | 105-107 | 3 | 8 |
| α-helix | 109-116 | 8 | |
| β-strand | 121-122 | 2 | 5 |
| β-strand | 127 | 1 | 9 |
| α-helix | 130-133 | 4 | |
| β-strand | 136-138 | 3 | 5 |
| α-helix | 139 | 1 | |
| α-helix | 141 | 1 | |
| β-strand | 143-152 | 10 | 9 |
| α-helix | 163-166 | 4 | |
| β-strand | 174-175 | 2 | 9 |
| β-strand | 177 | 1 | 10 |
| α-helix | 181-188 | 8 | |
| α-helix | 190-192 | 3 | |
| α-helix | 193-199 | 7 | |
| β-strand | 204 | 1 | 10 |
| α-helix | 207-215 | 9 | |
| β-strand | 221-225 | 5 | 9 |
| α-helix | 226-235 | 10 | |
| β-strand | 239-251 | 13 | 9 |
| β-strand | 254-256 | 3 | 5 |
| α-helix | 262-274 | 13 | |
| α-helix | 277-285 | 9 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Glutamate receptor ionotropic, NMDA 2A | A | protein | 285 | Homo sapiens | Q12879 (AlphaFold model) |
| Glutamate receptor ionotropic, NMDA 1 | B | protein | 293 | Homo sapiens | Q05586 (AlphaFold model) |
>5I2N_1 Glutamate receptor ionotropic, NMDA 2A (chains A) GSPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKG FCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEER SEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNN YPYMHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFA TTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHN
>5I2N_2 Glutamate receptor ionotropic, NMDA 1 (chains B) GSMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTV PQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQAD MIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQS SVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLV TTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDS
| ID | Name | Formula | Copies |
|---|---|---|---|
| CA | Calcium ion | Ca | 1 |
| GLY | Glycine | C2 H5 N O2 | 1 |
| 67J | N-ethyl-7-{[2-fluoro-3-(trifluoromethyl)phenyl]methyl}-2-methyl-5-oxo-5H-[1,3]t… | C18 H15 F4 N3 O2 S | 1 |
| GLU | Glutamic acid | C5 H9 N O4 | 1 |
Water and common crystallization additives (EPE) are not listed.
Discovery of GluN2A-Selective NMDA Receptor Positive Allosteric Modulators (PAMs): Tuning Deactivation Kinetics via Structure-Based Design. Volgraf, M., Sellers, B.D., Jiang, Y. et al. J Med Chem (2016) 59:2760-2779. DOI 10.1021/acs.jmedchem.5b02010 · PubMed
Other PDB entries of the same protein (UniProt Q12879 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 5I2N directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.