MolNFT v1 · #45893 · protein
The structure of deoxycytidine kinase complexed with lamivudine and ADP.
2NOA: “The structure of deoxycytidine kinase complexed with lamivudine and ADP.”. X-ray diffraction, 2 ligands (ADP, 3TC), 4 pockets (best druggability 0.69). MolNFT v1 #45893 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2NOA
- Type
- protein
- Length
- 464 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
- ADP, 3TC
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxycytidine kinase (EC 2.7.1.74) | protein | 242 | 55% helix, 11% strand | P27707 |
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 222 | 57% helix, 12% strand | P27707 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- 3TC · 4-amino-1-[(2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]pyrimidin-2(1H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.69 | 0.87 | 40 | ADP, 3TC |
| 2 | 194 | 0.68 | 0.86 | 36 | ADP, 3TC |
| 3 | 194 | 0.44 | 0.73 | 29 | empty |
| 4 | 69 | 0.39 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1339 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2NOA · The structure of deoxycytidine kinase complexed with lamivudine and ADP. · 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 B 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 P27707
- Elsewhere: RCSB PDB 2NOA · PDBe 2NOA · UniProt P27707
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