Ligand profile

T04

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_2476 — UDP-N-acetylmuramate--alanine ligase

Via homolog PDB 2y68 UniProt P14900 Formula C₂₃H₂₀FN₃O₆S₂
Mol. weight 517.56 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
T04
PDB
2y68
UniProt (similar protein)
P14900
Target protein
VK055_2476

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 517.56 Da
LogP (Crippen) 2.97
H-bond donors 5
H-bond acceptors 7
TPSA 144.83 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 35
Fraction sp³ C 0.17
Formula C₂₃H₂₀FN₃O₆S₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 144.8
  • −1 ≤ LogP ≤ 5 2.97
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 517.6
  • LogP ≤ 5 2.97
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 144.8
PAINS Alert

Matches PAINS filter: ene_rhod_A(235). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1\C=C/2\C(=O)NC(=S)S2)NCc3ccc(c(c3)C(=O)NC(CCC(=O)O)C(=O)O)F
InChI 
InChI=1S/C23H20FN3O6S2/c24-16-6-3-13(9-15(16)20(30)26-17(22(32)33)7-8-19(28)29)11-25-14-4-1-12(2-5-14)10-18-21(31)27-23(34)35-18/h1-6,9-10,17,25H,7-8,11H2,(H,26,30)(H,28,29)(H,32,33)(H,27,31,34)/b18-10-
InChIKey 
NEGUDZMAJDITEM-ZDLGFXPLSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF02875' 'PF08245' 'PF21799

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_2476.

PDB 17

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)