MolNFT v1 · #180102 · protein
Asymmetric htnf-alpha
7KPA · Tumor necrosis factor: “Asymmetric htnf-alpha”. X-ray diffraction, 1 ligand (D84), 5 pockets (best druggability 0.80). MolNFT v1 #180102 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KPA
- Type
- protein
- Length
- 426 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor
- UniProt
- P01375
- Ligands
- D84
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor | protein | 147 | 0% helix, 52% strand | P01375 |
| B | Tumor necrosis factor | protein | 146 | 2% helix, 51% strand | P01375 |
| C | Tumor necrosis factor | protein | 133 | 5% helix, 56% strand | P01375 |
Ligands and binding sites
- D84 · 5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.80 | 0.87 | 63 | D84 |
| 2 | 488 | 0.71 | 0.80 | 52 | empty |
| 3 | 50 | 0.49 | 0.87 | 17 | empty |
| 4 | 105 | 0.48 | 0.80 | 21 | empty |
| 5 | 79 | 0.38 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1062 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1027 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 373 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7KPA · asymmetric hTNF-alpha · 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 7KPA · PDBe 7KPA · UniProt P01375
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