Research workbench
Crystal structure of TNF-alpha with a small molecule inhibitor
Analyse Crystal structure of TNF-alpha with a small molecule inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AZ5
- Type
- protein
- Length
- 542 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor (TNF-alpha) (tumor necrosis factor ligand superfamily member 2)…
- UniProt
- P01375
- Ligands
- 307
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor (TNF-alpha) (tumor necrosis factor ligand superfamily member 2) (TNF-a) (cachectin) [contains: tumor necrosis factor, membrane form | protein | 132 | 5% helix, 52% strand | P01375 |
| B | Tumor necrosis factor (TNF-alpha) (tumor necrosis factor ligand superfamily member 2) (TNF-a) (cachectin) [contains: tumor necrosis factor, membrane form | protein | 140 | 2% helix, 53% strand | P01375 |
| C | Tumor necrosis factor (TNF-alpha) (tumor necrosis factor ligand superfamily member 2) (TNF-a) (cachectin) [contains: tumor necrosis factor, membrane form | protein | 129 | 2% helix, 55% strand | P01375 |
| D | Tumor necrosis factor (TNF-alpha) (tumor necrosis factor ligand superfamily member 2) (TNF-a) (cachectin) [contains: tumor necrosis factor, membrane form | protein | 141 | 2% helix, 55% strand | P01375 |
Ligands and binding sites
- 307 · 6,7-dimethyl-3-[(methyl{2-[methyl({1-[3-(trifluoromethyl)phenyl]-1H-indol-3-yl}methyl)amino]ethyl}amino)methyl]-4H-chromen-4-one · ligand · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.56 | 0.75 | 32 | 307 |
| 2 | 330 | 0.56 | 0.75 | 36 | 307 |
| 3 | 236 | 0.55 | 0.78 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–B · 926 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 919 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 340 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2AZ5 · Crystal Structure of TNF-alpha with a small molecule 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 P01375
- Elsewhere: RCSB PDB 2AZ5 · PDBe 2AZ5 · UniProt P01375
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