GL1X · GenesisL1 explorer

MolNFT v1 · #104631 · protein

S.AUREUS tmk in complex with potent inhibitor compound 47

4QGH · Thymidylate kinase: “S.AUREUS tmk in complex with potent inhibitor compound 47”. X-ray diffraction, 1 ligand (32E), 2 pockets (best druggability 0.76). MolNFT v1 #104631 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4QGH
Type
protein
Length
393 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
32E
Pockets
2 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 60% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AThymidylate kinase (EC 2.7.4.9)protein19559% helix, 14% strandQ6GJI9
BThymidylate kinase (EC 2.7.4.9)protein19861% helix, 14% strandQ6GJI9

Ligands and binding sites

  • 32E · 2-(3-chlorophenoxy)-3-fluoro-4-{(1S)-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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19370.760.797132E
21960.520.782432E

Interfaces

1 interface between chains.

  • A–B · 171 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

  • 4QGH · S.aureus TMK in complex with potent inhibitor compound 47 · 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 A against A, TM-score 0.95

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