MolNFT v1 · #120998 · protein
Binding site elucidation and structure guided design of macrocyclic il-17A antagonists
5HI3 · Interleukin-17A: “Binding site elucidation and structure guided design of macrocyclic il-17A antagonists”. X-ray diffraction, 1 ligand (63O), 14 pockets (best druggability 0.76). MolNFT v1 #120998 on GenesisL1: 3D structure, binding…
- PDB
- 5HI3
- Type
- protein
- Length
- 1,068 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-17A; Cat-2000 Fab heavy chain; Cat-2000 Fab light chain; Synthetic il-17A…
- UniProt
- Q16552
- Ligands
- 63O
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-17A | protein | 100 | 4% helix, 53% strand | Q16552 |
| B | Interleukin-17A | protein | 88 | 5% helix, 57% strand | Q16552 |
| C, H | Cat-2000 Fab heavy chain | protein | 220 | 10% helix, 53% strand | — |
| D, L | Cat-2000 Fab light chain | protein | 213 | 8% helix, 50% strand | — |
| I | Synthetic il-17A peptide inhibitor | protein | 14 | 50% helix, 36% strand | — |
Ligands and binding sites
- 63O · N-(4-{2-[({1-[2-(dimethylamino)-2-oxoethyl]cyclopentyl}acetyl)amino]ethyl}phenyl)-2-fluoro-Nalpha-[(1-methyl-1H-pyrazol-5-yl)carbonyl]-L-phenylalaninamide · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.76 | 0.78 | 95 | 63O |
| 2 | 266 | 0.66 | 0.82 | 47 | empty |
| 3 | 451 | 0.58 | 0.74 | 61 | empty |
| 4 | 138 | 0.55 | 0.82 | 35 | empty |
| 5 | 347 | 0.54 | 0.74 | 38 | empty |
Interfaces
11 interfaces between chains.
- H–L · 1847 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1802 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1174 Ų buried · 13 hydrogen bonds · protein-protein
- A–I · 669 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 363 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5HI3 · Binding site elucidation and structure guided design of macrocyclic IL-17A antagonists · the same entry in another collection · chain L against L, TM-score 1.00
- Q16552 · AlphaFold monomer V2.0 prediction for interleukin-17A (Q16552) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 Q16552
- Elsewhere: RCSB PDB 5HI3 · PDBe 5HI3 · UniProt Q16552
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.