Research workbench
Crystal structure of dck mutant C3S in complex with masitinib and udp
Analyse Crystal structure of dck mutant C3S in complex with masitinib and udp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MQL
- Type
- protein
- Length
- 911 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxycytidine kinase
- EC
- 2.7.1.74
- UniProt
- P27707
- Ligands
- UDP, DCM, G65, MG
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxycytidine kinase (EC 2.7.1.74) | protein | 231 | 55% helix, 11% strand | P27707 |
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 227 | 52% helix, 11% strand | P27707 |
| C | Deoxycytidine kinase (EC 2.7.1.74) | protein | 228 | 54% helix, 12% strand | P27707 |
| D | Deoxycytidine kinase (EC 2.7.1.74) | protein | 225 | 55% helix, 12% strand | P27707 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- DCM · 2'-deoxycytidine-5'-monophosphate · ligand · 2 copies · chains B, C
- G65 · Masitinib · ligand · chains A
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.81 | 0.83 | 90 | MG, UDP, DCM |
| 2 | 417 | 0.75 | 0.84 | 41 | UDP, G65 |
| 3 | 444 | 0.70 | 0.80 | 37 | UDP |
| 4 | 162 | 0.67 | 0.87 | 32 | UDP, DCM |
| 5 | 91 | 0.38 | 0.76 | 14 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1310 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1283 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 75 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MQL · Crystal structure of dCK mutant C3S in complex with masitinib and UDP · the same entry in another collection · chain D against D, 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 5MQL · PDBe 5MQL · UniProt P27707
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