MolNFT v1 · #171642 · protein
Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor and sybody SB_GLYT1#7
6ZBV · Sodium- and chloride-dependent glycine transporter 1…: “Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor and…”. X-ray diffraction, 1 ligand (QET), 7 pockets (best druggability…
- PDB
- 6ZBV
- Type
- protein
- Length
- 659 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium- and chloride-dependent glycine transporter 1, sodium- and chloride-dependent…
- UniProt
- P48067
- Ligands
- QET
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium- and chloride-dependent glycine transporter 1, sodium- and chloride-dependent glycine transporter 1 | protein | 539 | 69% helix, 1% strand | P48067 |
| B | Sybody SB_GLYT1#7 | protein | 120 | 5% helix, 52% strand | — |
Ligands and binding sites
- QET · [5-fluoranyl-6-(oxan-4-yloxy)-1,3-dihydroisoindol-2-yl]-[5-methylsulfonyl-2-[2,2,3,3,3-pentakis(fluoranyl)propoxy]phenyl]methanone · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.74 | 0.82 | 55 | QET |
| 2 | 385 | 0.67 | 0.80 | 42 | empty |
| 3 | 157 | 0.57 | 0.81 | 24 | empty |
| 4 | 53 | 0.36 | 0.79 | 12 | empty |
| 5 | 50 | 0.30 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 822 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6ZBV · Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline… · the same entry in another collection · chain A against A, TM-score 1.00
- P48067 · AlphaFold monomer V2.0 prediction for sodium- and chloride-dependent glycine transporter… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P48067
- Elsewhere: RCSB PDB 6ZBV · PDBe 6ZBV · UniProt P48067
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