Research workbench
Crystal structure of tnfalpha with isoquinoline compound 2
Analyse Crystal structure of tnfalpha with isoquinoline compound 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X81
- Type
- protein
- Length
- 852 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor
- UniProt
- P01375
- Ligands
- UTJ
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 1% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor | protein | 145 | 2% helix, 52% strand | P01375 |
| B | Tumor necrosis factor | protein | 146 | 0% helix, 50% strand | P01375 |
| C | Tumor necrosis factor | protein | 144 | 0% helix, 52% strand | P01375 |
| D | Tumor necrosis factor | protein | 141 | 4% helix, 53% strand | P01375 |
| E | Tumor necrosis factor | protein | 132 | 2% helix, 52% strand | P01375 |
| F | Tumor necrosis factor | protein | 144 | 0% helix, 51% strand | P01375 |
Ligands and binding sites
- UTJ · [4-(isoquinolin-8-yl)phenyl]acetonitrile · ligand · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.85 | 0.93 | 52 | UTJ |
| 2 | 1002 | 0.83 | 0.84 | 80 | empty |
| 3 | 382 | 0.82 | 0.91 | 45 | UTJ |
| 4 | 423 | 0.76 | 0.85 | 46 | empty |
| 5 | 751 | 0.74 | 0.79 | 70 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1193 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1065 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1003 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 897 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 656 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6X81 · Crystal Structure of TNFalpha with isoquinoline compound 2 · 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 P01375
- Elsewhere: RCSB PDB 6X81 · PDBe 6X81 · UniProt P01375
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