MolNFT v1 · #88648 · protein
Structure of MHP1, a nucleobase-cation-symport-1 family transporter with the inhibitor 5-(2-naphthylmethyl)-L-hydantoin.
4D1D · Hydantoin transport protein: “Structure of MHP1, a nucleobase-cation-symport-1 family transporter with the inhibitor…”. X-ray diffraction, 3 ligands (5NL, 5ND, NA), 6 pockets (best druggability 0.75). MolNFT v1 #88648 on GenesisL1…
- PDB
- 4D1D
- Type
- protein
- Length
- 456 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydantoin transport protein
- UniProt
- D6R8X8
- Ligands
- 5NL, 5ND, NA
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydantoin transport protein | protein | 456 | 73% helix, 1% strand | D6R8X8 |
Ligands and binding sites
- 5NL · 5-(2-naphthylmethyl)-L-hydantoin · ligand · chains A
- 5ND · 5-(2-naphthylmethyl)-D-hydantoin · ligand · chains A
- NA · Sodium ion · metal · chains A
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 | 422 | 0.75 | 0.84 | 50 | 5NL, 5ND |
| 2 | 50 | 0.72 | 0.99 | 16 | empty |
| 3 | 108 | 0.59 | 0.85 | 18 | empty |
| 4 | 91 | 0.46 | 0.80 | 14 | empty |
| 5 | 94 | 0.41 | 0.78 | 24 | empty |
Compared structures
- 4D1D · STRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORTER with the inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- D6R8X8 · AlphaFold monomer V2.0 prediction for hydantoin permease (D6R8X8) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 D6R8X8
- Elsewhere: RCSB PDB 4D1D · PDBe 4D1D · UniProt D6R8X8
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