MolNFT v1 · #28540 · protein
Crystal structure of pyridoxal kinase in complex with roscovitine and derivatives
1YHJ: “Crystal structure of pyridoxal kinase in complex with roscovitine and derivatives”. X-ray diffraction, 1 ligand (R6C), 2 pockets (best druggability 0.77). MolNFT v1 #28540 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1YHJ
- Type
- protein
- Length
- 307 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal kinase
- EC
- 2.7.1.35
- UniProt
- P82197
- Ligands
- R6C
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase (EC 2.7.1.35) | protein | 307 | 39% helix, 18% strand | P82197 |
Ligands and binding sites
- R6C · (2R)-2-{[6-(benzyloxy)-9-isopropyl-9H-purin-2-yl]amino}butan-1-ol · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.77 | 0.81 | 62 | R6C |
| 2 | 73 | 0.34 | 0.76 | 16 | empty |
Compared structures
- 1YHJ · Crystal Structure of Pyridoxal Kinase in Complex with Roscovitine and Derivatives · the same entry in another collection · chain A against A, TM-score 1.00
- P82197 · AlphaFold monomer V2.0 prediction for pyridoxal kinase (P82197) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P82197
- Elsewhere: RCSB PDB 1YHJ · PDBe 1YHJ · UniProt P82197
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