Ligand profile

ZINC4962415

Virtual-screening candidate from ZINC.

Bound to: VK055_0456 — bacterial extracellular solute-binding, 5 Middlefamily protein

Via homolog UniProt B8F653 Formula C₁₉H₂₅N₃O₇S
Tanimoto 0.65
Mol. weight 439.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4962415
UniProt (similar protein)
B8F653
Tanimoto
0.647
Target protein
VK055_0456

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 439.49 Da
LogP (Crippen) -0.13
H-bond donors 5
H-bond acceptors 7
TPSA 175.89 Ų
Rotatable bonds 14
Aromatic rings 1 / 1
Heavy atoms 30
Fraction sp³ C 0.42
Formula C₁₉H₂₅N₃O₇S

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 175.9
  • −1 ≤ LogP ≤ 5 -0.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 439.5
  • LogP ≤ 5 -0.13
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 175.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@H](CCC(=O)N[C@@H](CSCCC(=O)c1ccccc1)C(=O)NCC(=O)O)C(=O)O
InChI 
InChI=1S/C19H25N3O7S/c20-13(19(28)29)6-7-16(24)22-14(18(27)21-10-17(25)26)11-30-9-8-15(23)12-4-2-1-3-5-12/h1-5,13-14H,6-11,20H2,(H,21,27)(H,22,24)(H,25,26)(H,28,29)/t13-,14+/m1/s1
InChIKey 
SFDCSAYAWIDXIJ-KGLIPLIRSA-N

Provenance

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

Method
LigQ nearest_k
Query
GDS
Homolog
B8F653

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_0456.

PDB 4

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)