Research workbench
PICK1 PDZ domain in complex with the small molecule inhibitor BIO124.
Analyse PICK1 PDZ domain in complex with the small molecule inhibitor BIO124. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BJO
- Type
- protein
- Length
- 171 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prkca-binding protein
- UniProt
- Q9NRD5
- Ligands
- DUY
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prkca-binding protein | protein | 86 | 16% helix, 43% strand | Q9NRD5 |
| B | Prkca-binding protein | protein | 85 | 16% helix, 38% strand | Q9NRD5 |
Ligands and binding sites
- DUY · (2S)-({4-(4-bromophenyl)-1-[1-(tert-butoxycarbonyl)-L-prolyl]piperidine-4-carbonyl}amino)(cyclopentyl)acetic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.41 | 0.80 | 14 | empty |
| 2 | 72 | 0.39 | 0.78 | 12 | empty |
| 3 | 52 | 0.30 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 460 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6BJO · PICK1 PDZ domain in complex with the small molecule inhibitor BIO124. · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NRD5 · AlphaFold monomer V2.0 prediction for prkca-binding protein (Q9NRD5) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9NRD5
- Elsewhere: RCSB PDB 6BJO · PDBe 6BJO · UniProt Q9NRD5
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