MolNFT v1 · #104624 · protein
S.AUREUS tmk in complex with potent inhibitor compound 19, 2-(3- chlorophenoxy)-3-fluoro-4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4- dihydropyrimidin-1(2H)-YL)PIPERIDIN-1-YL]METHYL}BENZOIC acid
4QGA · Thymidylate kinase: “S.AUREUS tmk in complex with potent inhibitor compound 19, 2-(3…”. X-ray diffraction, 1 ligand (31Z), 2 pockets (best druggability 0.56). MolNFT v1 #104624 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4QGA
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q6GJI9
- Ligands
- 31Z
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 196 | 60% helix, 14% strand | Q6GJI9 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 198 | 60% helix, 14% strand | Q6GJI9 |
Ligands and binding sites
- 31Z · 2-(3-chlorophenoxy)-3-fluoro-4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]methyl}benzoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.56 | 0.76 | 35 | 31Z |
| 2 | 191 | 0.52 | 0.78 | 24 | 31Z |
Interfaces
1 interface between chains.
- A–B · 1049 Ų buried · 12 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 Q6GJI9
- Elsewhere: RCSB PDB 4QGA · PDBe 4QGA · UniProt Q6GJI9
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