MolNFT v1 · #127242 · protein
Crystal structure of dck mutant C3S in complex with imatinib and udp
5MQT · Deoxycytidine kinase: “Crystal structure of dck mutant C3S in complex with imatinib and udp”. X-ray diffraction, 4 ligands (UDP, STI, DCM), 9 pockets (best druggability 0.72). MolNFT v1 #127242 on GenesisL1: 3D structure, binding…
- PDB
- 5MQT
- Type
- protein
- Length
- 915 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, STI, DCM, MG
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxycytidine kinase (EC 2.7.1.74) | protein | 230 | 59% helix, 11% strand | P27707 |
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 229 | 55% helix, 11% strand | P27707 |
| C | Deoxycytidine kinase (EC 2.7.1.74) | protein | 230 | 56% helix, 11% strand | P27707 |
| D | Deoxycytidine kinase (EC 2.7.1.74) | protein | 226 | 60% helix, 12% strand | P27707 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- STI · 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-benzamide · ligand · 2 copies · chains A, C
- DCM · 2'-deoxycytidine-5'-monophosphate · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.72 | 0.88 | 35 | UDP, DCM |
| 2 | 355 | 0.72 | 0.84 | 43 | UDP, STI |
| 3 | 380 | 0.72 | 0.83 | 41 | UDP, STI |
| 4 | 178 | 0.67 | 0.86 | 33 | MG, UDP, DCM |
| 5 | 332 | 0.53 | 0.74 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1278 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1190 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 483 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5MQT · Crystal structure of dCK mutant C3S in complex with imatinib 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 5MQT · PDBe 5MQT · UniProt P27707
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