MolNFT v1 · #67628 · protein
X-ray structure of human deoxycytidine kinase in complex with ADP and an inhibitor
3IPX: “X-ray structure of human deoxycytidine kinase in complex with ADP and an inhibitor”. X-ray diffraction, 3 ligands (ADP, B86, MG), 2 pockets (best druggability 0.66). MolNFT v1 #67628 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3IPX
- Type
- protein
- Length
- 229 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxycytidine kinase
- EC
- 2.7.1.74
- UniProt
- P27707
- Ligands
- ADP, B86, MG
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxycytidine kinase (EC 2.7.1.74) | protein | 229 | 57% helix, 12% strand | P27707 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- B86 · 2'-deoxy-5-fluorocytidine · ligand · chains A
- MG · Magnesium ion · metal · 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 | 211 | 0.66 | 0.84 | 37 | ADP, B86, MG |
| 2 | 66 | 0.34 | 0.76 | 16 | empty |
Compared structures
- 3IPX · X-Ray structure of Human Deoxycytidine Kinase in complex with ADP and an 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 0.99
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 3IPX · PDBe 3IPX · UniProt P27707
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