MolNFT v1 · #127234 · protein
Crystal structure of dck mutant C3S in complex with masitinib and udp
5MQL · Deoxycytidine kinase: “Crystal structure of dck mutant C3S in complex with masitinib and udp”. X-ray diffraction, 4 ligands (UDP, DCM, G65), 8 pockets (best druggability 0.81). MolNFT v1 #127234 on GenesisL1: 3D structure, binding…
- 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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