MolNFT v1 · #97393 · protein
Human dck C4S-S74E mutant in complex with udp and the di-39 inhibitor
4KCG · Deoxycytidine kinase: “Human dck C4S-S74E mutant in complex with udp and the di-39 inhibitor”. X-ray diffraction, 2 ligands (1QC, UDP), 2 pockets (best druggability 0.74). MolNFT v1 #97393 on GenesisL1: 3D structure, binding sites…
- PDB
- 4KCG
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxycytidine kinase
- EC
- 2.7.1.74
- UniProt
- P27707
- Ligands
- 1QC, UDP
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxycytidine kinase (EC 2.7.1.74) | protein | 230 | 59% helix, 11% strand | P27707 |
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 230 | 54% helix, 11% strand | P27707 |
Ligands and binding sites
- 1QC · N-{2-[5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethyl}methanesulfonamide · ligand · 2 copies · chains A, B
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.74 | 0.85 | 43 | 1QC, UDP |
| 2 | 361 | 0.72 | 0.84 | 43 | 1QC, UDP |
Interfaces
1 interface between chains.
- A–B · 1298 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4KCG · Human dCK C4S-S74E mutant in complex with UDP and the DI-39 inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P27707 · AlphaFold monomer V2.0 prediction for deoxycytidine kinase (P27707) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P27707
- Elsewhere: RCSB PDB 4KCG · PDBe 4KCG · UniProt P27707
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