Research workbench
Tetrahydroquinoline carboxylates are potent inhibitors of the shank PDZ domain, a putative target in autism disorders
Analyse Tetrahydroquinoline carboxylates are potent inhibitors of the shank PDZ domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O5N
- Type
- protein
- Length
- 772 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SH3 and multiple ankyrin repeat domains protein 3
- UniProt
- Q4ACU6
- Ligands
- BR0
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SH3 and multiple ankyrin repeat domains protein 3 | protein | 100 | 13% helix, 38% strand | Q4ACU6 |
| B | SH3 and multiple ankyrin repeat domains protein 3 | protein | 98 | 12% helix, 43% strand | Q4ACU6 |
| C | SH3 and multiple ankyrin repeat domains protein 3 | protein | 97 | 15% helix, 41% strand | Q4ACU6 |
| D | SH3 and multiple ankyrin repeat domains protein 3 | protein | 100 | 16% helix, 29% strand | Q4ACU6 |
| E | SH3 and multiple ankyrin repeat domains protein 3 | protein | 92 | 14% helix, 33% strand | Q4ACU6 |
| F | SH3 and multiple ankyrin repeat domains protein 3 | protein | 97 | 11% helix, 39% strand | Q4ACU6 |
| G | SH3 and multiple ankyrin repeat domains protein 3 | protein | 95 | 15% helix, 39% strand | Q4ACU6 |
| H | SH3 and multiple ankyrin repeat domains protein 3 | protein | 93 | 14% helix, 28% strand | Q4ACU6 |
Ligands and binding sites
- BR0 · (3aS,4R,9bR)-9-nitro-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-4,6-dicarboxylic acid · ligand · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.79 | 0.80 | 123 | empty |
| 2 | 1084 | 0.74 | 0.77 | 80 | BR0 |
| 3 | 350 | 0.53 | 0.73 | 40 | empty |
| 4 | 134 | 0.48 | 0.78 | 16 | empty |
| 5 | 179 | 0.45 | 0.75 | 23 | empty |
Interfaces
13 interfaces between chains.
- B–G · 678 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 582 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 531 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 485 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 470 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3O5N · Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a… · the same entry in another collection · chain H against H, TM-score 1.00
- Q4ACU6 · AlphaFold monomer V2.0 prediction for SH3 and multiple ankyrin repeat domains protein 3… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q4ACU6
- Elsewhere: RCSB PDB 3O5N · PDBe 3O5N · UniProt Q4ACU6
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