Research workbench
Crystal structure of tnfalpha with indolinone compound 11
Analyse Crystal structure of tnfalpha with indolinone compound 11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X86
- Type
- protein
- Length
- 841 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor
- UniProt
- P01375
- Ligands
- UTY
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor | protein | 151 | 4% helix, 52% strand | P01375 |
| B | Tumor necrosis factor | protein | 130 | 2% helix, 55% strand | P01375 |
| C | Tumor necrosis factor | protein | 142 | 2% helix, 49% strand | P01375 |
| D | Tumor necrosis factor | protein | 139 | 2% helix, 51% strand | P01375 |
| E | Tumor necrosis factor | protein | 135 | 2% helix, 50% strand | P01375 |
| F | Tumor necrosis factor | protein | 144 | 2% helix, 52% strand | P01375 |
Ligands and binding sites
- UTY · 3-[(6-{2-[(3R)-4-(hydroxyacetyl)-3-methylpiperazin-1-yl]pyrimidin-5-yl}-2,2-dimethyl-3-oxo-2,3-dihydro-1H-indol-1-yl)methyl]pyridine-2-carbonitrile · ligand · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.81 | 0.91 | 38 | UTY |
| 2 | 699 | 0.80 | 0.84 | 72 | empty |
| 3 | 767 | 0.80 | 0.83 | 71 | empty |
| 4 | 415 | 0.79 | 0.87 | 56 | UTY |
| 5 | 655 | 0.78 | 0.83 | 70 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1199 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1186 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1048 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 935 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 628 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6X86 · Crystal Structure of TNFalpha with indoli compound 11 · 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 6X86 · PDBe 6X86 · UniProt P01375
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