Research workbench
Human TNF-alpha in complex with 2-[5-(3-chloro-4-{[(1R)-1-(2- FLUOROPHENYL)ETHYL]AMINO}QUINOLIN-6-YL)PYRIMIDIN-2-YL]PROPAN-2-ol
Analyse Human TNF-alpha in complex with 2-[5-(3-chloro-4-{[(1R)-1-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JRA
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor
- UniProt
- P01375
- Ligands
- VGY
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor | protein | 153 | 2% helix, 52% strand | P01375 |
| B | Tumor necrosis factor | protein | 146 | 2% helix, 53% strand | P01375 |
| C | Tumor necrosis factor | protein | 142 | 2% helix, 53% strand | P01375 |
Ligands and binding sites
- VGY · 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl) ethyl]amino}quinolin-6-yl)pyrimidin-2-yl]propan-2-ol · ligand · chains A, B, C
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.79 | 0.88 | 45 | VGY |
| 2 | 790 | 0.76 | 0.80 | 81 | GOL |
| 3 | 59 | 0.57 | 0.89 | 19 | empty |
| 4 | 103 | 0.47 | 0.80 | 20 | empty |
| 5 | 50 | 0.40 | 0.82 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1025 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 926 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 432 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7JRA · HUMAN TNF-ALPHA IN COMPLEX WITH 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}quin… · 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 7JRA · PDBe 7JRA · UniProt P01375
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