MolNFT v1 · #20380 · protein
An allosteric inhibitor of lfa-1 bound to its I-domain
1RD4 · Integrin alpha-L: “An allosteric inhibitor of lfa-1 bound to its I-domain”. X-ray diffraction, 1 ligand (L08), 9 pockets (best druggability 0.72). MolNFT v1 #20380 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1RD4
- Type
- protein
- Length
- 736 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-L
- UniProt
- P20701
- Ligands
- L08
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Integrin alpha-L | protein | 184 | 36% helix, 23% strand | P20701 |
Ligands and binding sites
- L08 · 1-acetyl-4-(4-{4-[(2-ethoxyphenyl)thio]-3-nitrophenyl}pyridin-2-yl)piperazine · ligand · 4 copies · chains A, B, C, D
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 | 265 | 0.72 | 0.85 | 28 | L08 |
| 2 | 272 | 0.71 | 0.85 | 30 | L08 |
| 3 | 293 | 0.66 | 0.81 | 28 | L08 |
| 4 | 251 | 0.65 | 0.82 | 27 | L08 |
| 5 | 543 | 0.64 | 0.76 | 58 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1191 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 425 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 191 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P20701
- Elsewhere: RCSB PDB 1RD4 · PDBe 1RD4 · UniProt P20701
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