Ligand profile

YF3

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

Bound to: VK055_0407 — acetolactate synthase, catabolic

Via homolog PDB 1t9a UniProt P07342 Formula C₉H₁₆N₄S
Mol. weight 212.32 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
YF3
PDB
1t9a
UniProt (similar protein)
P07342
Target protein
VK055_0407

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 212.32 Da
LogP (Crippen) 0.78
H-bond donors 3
H-bond acceptors 5
TPSA 63.83 Ų
Rotatable bonds 4
Aromatic rings 1 / 1
Heavy atoms 14
Fraction sp³ C 0.56
Formula C₉H₁₆N₄S

Drug-likeness

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

Permeability proxy High

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 63.8
  • −1 ≤ LogP ≤ 5 0.78
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 212.3
  • LogP ≤ 5 0.78
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 63.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ncc(c(n1)N)CNC(C)CS
InChI 
InChI=1S/C9H16N4S/c1-6(5-14)11-3-8-4-12-7(2)13-9(8)10/h4,6,11,14H,3,5H2,1-2H3,(H2,10,12,13)
InChIKey 
BGGAKPFEDJLRDQ-UHFFFAOYSA-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
PF02775' 'PF02776

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_0407.

PDB 38

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

Ligand PDB entry

ChEMBL 37

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)