MolNFT v1 · #67629 · protein
X-ray structure of human deoxycytidine kinase in complex with an inhibitor
3IPY: “X-ray structure of human deoxycytidine kinase in complex with an inhibitor”. X-ray diffraction, 2 ligands (B87, MLT), 3 pockets (best druggability 0.73). MolNFT v1 #67629 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IPY
- Type
- protein
- Length
- 450 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
- B87, MLT
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 225 | 58% helix, 12% strand | P27707 |
Ligands and binding sites
- B87 · 4-(1-benzothiophen-2-yl)-6-[4-(2-oxo-2-pyrrolidin-1-ylethyl)piperazin-1-yl]pyrimidine · ligand · 4 copies · chains A, B
- MLT · D-malate · 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 | 437 | 0.73 | 0.83 | 39 | MLT, B87 |
| 2 | 419 | 0.73 | 0.83 | 38 | MLT, B87 |
| 3 | 59 | 0.46 | 0.84 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1128 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3IPY · X-Ray structure of Human Deoxycytidine Kinase in complex with 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 B against A, TM-score 0.96
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 3IPY · PDBe 3IPY · UniProt P27707
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