MolNFT v1 · #169315 · protein
Crystal structure of tnfalpha with indolinone compound 9
6X85 · Tumor necrosis factor: “Crystal structure of tnfalpha with indolinone compound 9”. X-ray diffraction, 1 ligand (UTV), 11 pockets (best druggability 0.82). MolNFT v1 #169315 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6X85
- Type
- protein
- Length
- 838 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor
- UniProt
- P01375
- Ligands
- UTV
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 2% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor | protein | 148 | 2% helix, 48% strand | P01375 |
| B | Tumor necrosis factor | protein | 129 | 2% helix, 56% strand | P01375 |
| C, F | Tumor necrosis factor | protein | 144 | 2% helix, 50% strand | P01375 |
| D | Tumor necrosis factor | protein | 138 | 2% helix, 51% strand | P01375 |
| E | Tumor necrosis factor | protein | 135 | 2% helix, 50% strand | P01375 |
Ligands and binding sites
- UTV · 1-{[2-(difluoromethoxy)phenyl]methyl}-2,2-dimethyl-1,2-dihydro-3H-indol-3-one · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.82 | 0.83 | 102 | empty |
| 2 | 266 | 0.80 | 0.91 | 38 | UTV |
| 3 | 890 | 0.79 | 0.82 | 91 | empty |
| 4 | 74 | 0.75 | 0.98 | 17 | empty |
| 5 | 312 | 0.67 | 0.82 | 37 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1200 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1141 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1089 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1022 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 747 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6X85 · Crystal Structure of TNFalpha with indoli compound 9 · 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 6X85 · PDBe 6X85 · UniProt P01375
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