MolNFT v1 · #111001 · protein
High resolution crystal structure of human transthyretin bound to ligand and conjugates of 4-(5-(3,5-dichloro-4-hydroxyphenyl)-1,3,4- oxadiazol-2-YL)PHENYL fluorosulfate
4YDN: “High resolution crystal structure of human transthyretin bound to ligand and conjugates of…”. X-ray diffraction, 2 ligands (2WN, 4B8), 2 pockets (best druggability 0.32). MolNFT v1 #111001 on GenesisL1: 3D structure, binding sites…
- PDB
- 4YDN
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transthyretin
- UniProt
- P02766
- Ligands
- 2WN, 4B8
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transthyretin | protein | 116 | 6% helix, 53% strand | P02766 |
| B | Transthyretin | protein | 115 | 6% helix, 53% strand | P02766 |
Ligands and binding sites
- 2WN · 4-[5-(3,5-dichloro-4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl]phenyl sulfurofluoridate · ligand · 2 copies · chains A, B
- 4B8 · 2,6-dichloro-4-[5-(4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl]phenol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.32 | 0.76 | 18 | empty |
| 2 | 53 | 0.32 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 911 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4YDN · High resolution crystal structure of human transthyretin bound to ligand and conjugates… · 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 P02766
- Elsewhere: RCSB PDB 4YDN · PDBe 4YDN · UniProt P02766
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