MolNFT v1 · #96506 · protein
Human dck C4S-S74E mutant in complex with udp and the F2.3.1 inhibitor (2-[({5-ethyl-2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-1,3-thiazol-4- YL}METHYL)SULFANYL]PYRIMIDINE-4,6-diamine)
4JLM · Deoxycytidine kinase: “Human dck C4S-S74E mutant in complex with udp and the F2.3.1 inhibitor…”. X-ray diffraction, 2 ligands (1NN, UDP), 3 pockets (best druggability 0.74). MolNFT v1 #96506 on GenesisL1: 3D structure, binding sites…
- PDB
- 4JLM
- Type
- protein
- Length
- 466 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
- 1NN, UDP
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 233 | 56% helix, 11% strand | P27707 |
Ligands and binding sites
- 1NN · 2-[({5-ethyl-2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-1,3-thiazol-4-yl}methyl)sulfanyl]pyrimidine-4,6-diamine · ligand · 3 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.74 | 0.83 | 46 | 1NN, UDP |
| 2 | 442 | 0.72 | 0.82 | 46 | 1NN, UDP |
| 3 | 60 | 0.47 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1279 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4JLM · Human dCK C4S-S74E mutant in complex with UDP and the F2.3.1 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 0.94
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 4JLM · PDBe 4JLM · UniProt P27707
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