MolNFT v1 · #121681 · protein
Structure of the human GLUN1/GLUN2A lbd in complex with 7-{[ETHYL(4- FLUOROPHENYL)AMINO]METHYL}-N,2-dimethyl-5-oxo-5H-[1,3]THIAZOLO[3,2- A]PYRIMIDINE-3-carboxamide (compound 19)
5I2K · Glutamate receptor ionotropic, NMDA 2A: “Structure of the human GLUN1/GLUN2A lbd in complex with 7-{[ETHYL(4…”. X-ray diffraction, 3 ligands (GLU, GLY, 67H), 7 pockets (best druggability 0.77). MolNFT v1 #121681 on GenesisL1: 3D…
- PDB
- 5I2K
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 2A; Glutamate receptor ionotropic, NMDA 1
- UniProt
- Q12879, Q05586
- Ligands
- GLU, GLY, 67H
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 2A | protein | 276 | 33% helix, 28% strand | Q12879 |
| B | Glutamate receptor ionotropic, NMDA 1 | protein | 286 | 31% helix, 27% strand | Q05586 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · chains A
- GLY · Glycine · ligand · chains B
- 67H · 7-{[ethyl(4-fluorophenyl)amino]methyl}-N,2-dimethyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.77 | 0.81 | 81 | 67H |
| 2 | 196 | 0.67 | 0.86 | 27 | empty |
| 3 | 304 | 0.60 | 0.78 | 38 | empty |
| 4 | 168 | 0.54 | 0.80 | 37 | GLU |
| 5 | 56 | 0.52 | 0.88 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1088 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5I2K · Structure of the human GluN1/GluN2A LBD in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q12879 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q12879) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q05586 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (Q05586) · a predicted model of the same protein · chain B against A, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q12879
- Every structure of UniProt Q05586
- Elsewhere: RCSB PDB 5I2K · PDBe 5I2K · UniProt Q12879 · UniProt Q05586
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