Research workbench
Crystal structure of human PIN1 complexed with a potent covalent inhibitor
Analyse Crystal structure of human PIN1 complexed with a potent covalent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F0M
- Type
- protein
- Length
- 584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase nima-interacting 1
- EC
- 5.2.1.8
- UniProt
- Q13526
- Ligands
- 0BF
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidyl-prolyl cis-trans isomerase nima-interacting 1 (EC 5.2.1.8) | protein | 146 | 27% helix, 26% strand | Q13526 |
Ligands and binding sites
- 0BF · 8-(2-chloranylethanoyl)-4-[(5-naphthalen-1-ylfuran-2-yl)methyl]-1-thia-4,8-diazaspiro[4.5]decan-3-one · ligand · 4 copies · chains A, C, B, D
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 4 copies · chains A, B, C, D
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 | 827 | 0.76 | 0.80 | 77 | P33, 0BF |
| 2 | 837 | 0.74 | 0.78 | 72 | 0BF, P33 |
| 3 | 347 | 0.61 | 0.78 | 42 | empty |
| 4 | 56 | 0.33 | 0.77 | 19 | P33 |
| 5 | 63 | 0.32 | 0.75 | 17 | 0BF |
Interfaces
3 interfaces between chains.
- B–D · 573 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 556 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 252 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7F0M · Crystal Structure of human Pin1 complexed with a potent covalent inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
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 Q13526
- Elsewhere: RCSB PDB 7F0M · PDBe 7F0M · UniProt Q13526
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