GL1X · GenesisL1 explorer

MolNFT v1 · #92666 · protein

Thymidylate kinase (tmk) from S. aureus in complex with tk-666

4GFD: “Thymidylate kinase (tmk) from S. aureus in complex with tk-666”. X-ray diffraction, 1 ligand (0YB), 2 pockets (best druggability 0.52). MolNFT v1 #92666 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4GFD
Type
protein
Length
382 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Thymidylate kinase
EC
2.7.4.9
UniProt
P65249
Ligands
0YB
Pockets
2 · best druggability 0.52

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
AThymidylate kinase (EC 2.7.4.9)protein18960% helix, 14% strandP65249
BThymidylate kinase (EC 2.7.4.9)protein19360% helix, 14% strandP65249

Ligands and binding sites

  • 0YB · 2-(3-bromophenoxy)-4-{(1R)-3,3-dimethyl-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
11700.520.79230YB
21720.500.78230YB

Interfaces

1 interface between chains.

  • A–B · 1049 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

  • 4GFD · Thymidylate kinase (TMK) from S. Aureus in complex with TK-666 · the same entry in another collection · chain A against A, TM-score 1.00
  • P65249 · AlphaFold monomer V2.0 prediction for thymidylate kinase (P65249) · a predicted model of the same protein · chain B against A, TM-score 0.96

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.