MolNFT v1 · #128471 · protein
Mtb tmk crystal structure in complex with compound 43
5NR7 · Thymidylate kinase: “Mtb tmk crystal structure in complex with compound 43”. X-ray diffraction, 2 ligands (YUI, CL), 3 pockets (best druggability 0.58). MolNFT v1 #128471 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NR7
- Type
- protein
- Length
- 372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- P9WKE1
- Ligands
- YUI, CL
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 188 | 52% helix, 13% strand | P9WKE1 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 184 | 54% helix, 13% strand | P9WKE1 |
Ligands and binding sites
- YUI · 1-[1-[[4-(3-chloranylphenoxy)quinolin-2-yl]methyl]piperidin-4-yl]-5-methyl-pyrimidine-2,4-dione · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 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 | 193 | 0.58 | 0.81 | 23 | YUI |
| 2 | 159 | 0.57 | 0.81 | 22 | YUI |
| 3 | 117 | 0.38 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 837 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
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 P9WKE1
- Elsewhere: RCSB PDB 5NR7 · PDBe 5NR7 · UniProt P9WKE1
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