Ligand profile

T03

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 3iu8 UniProt P9WK19 Formula C₉H₈FN₃S
Mol. weight 209.25 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
T03
PDB
3iu8
UniProt (similar protein)
P9WK19
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 209.25 Da
LogP (Crippen) 2.24
H-bond donors 1
H-bond acceptors 3
TPSA 41.57 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 14
Fraction sp³ C 0.11
Formula C₉H₈FN₃S

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 41.6
  • −1 ≤ LogP ≤ 5 2.24
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 209.2
  • LogP ≤ 5 2.24
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 41.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1CSc2[nH]cnn2)F
InChI 
InChI=1S/C9H8FN3S/c10-8-3-1-7(2-4-8)5-14-9-11-6-12-13-9/h1-4,6H,5H2,(H,11,12,13)
InChIKey 
XLRSDRUBTQOPEY-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
PF00557

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_2384.

PDB 45

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

Ligand PDB entry

ChEMBL 100

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)