MolNFT v1 · #104630 · protein
Tmk in complex with compound 46, 2-(3-chlorophenoxy)-3-fluoro-4-{(1R)- 3-methyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)- YL)PIPERIDIN-1-YL]BUTYL}BENZOIC acid
4QGG · Thymidylate kinase: “Tmk in complex with compound 46, 2-(3-chlorophenoxy)-3-fluoro-4-{(1R)…”. X-ray diffraction, 1 ligand (32C), 2 pockets (best druggability 0.53). MolNFT v1 #104630 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4QGG
- Type
- protein
- Length
- 388 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
- 32C
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 193 | 58% helix, 14% strand | Q6GJI9 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 195 | 60% helix, 13% strand | Q6GJI9 |
Ligands and binding sites
- 32C · 2-(3-chlorophenoxy)-3-fluoro-4-{(1R)-3-methyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}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 | 184 | 0.53 | 0.78 | 22 | 32C |
| 2 | 216 | 0.52 | 0.76 | 25 | 32C |
Interfaces
1 interface between chains.
- A–B · 1028 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4QGG · TMK in complex with compound 46, 2-(3-CHLOROPHENOXY)-3-FLUORO-4-{(1R)-3-METHYL-1-[(3S)-3-(… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GJI9 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q6GJI9) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 4QGG · PDBe 4QGG · UniProt Q6GJI9
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