MolNFT v1 · #45890 · protein
C4S dck variant of dck in complex with L-DC+ADP
2NO7 · Deoxycytidine kinase: “C4S dck variant of dck in complex with L-DC+ADP”. X-ray diffraction, 2 ligands (ADP, LDC), 3 pockets (best druggability 0.68). MolNFT v1 #45890 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2NO7
- Type
- protein
- Length
- 461 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, LDC
- Pockets
- 3 · best druggability 0.68
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 | 242 | 56% helix, 11% strand | P27707 |
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 219 | 57% helix, 12% strand | P27707 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- LDC · 4-amino-1-(2-deoxy-beta-L-erythro-pentofuranosyl)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
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 | 207 | 0.68 | 0.86 | 38 | ADP, LDC |
| 2 | 164 | 0.65 | 0.86 | 33 | ADP, LDC |
| 3 | 186 | 0.42 | 0.73 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1404 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 2NO7 · PDBe 2NO7 · UniProt P27707
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