Ligand profile

ZINC3874923

Virtual-screening candidate from ZINC.

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

Via homolog UniProt B8F653 Formula C₁₆H₂₉N₃O₆S
Tanimoto 0.67
Mol. weight 391.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3874923
UniProt (similar protein)
B8F653
Tanimoto
0.673
Target protein
VK055_0456

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 391.49 Da
LogP (Crippen) 0.18
H-bond donors 5
H-bond acceptors 6
TPSA 158.82 Ų
Rotatable bonds 15
Aromatic rings 0 / 0
Heavy atoms 26
Fraction sp³ C 0.75
Formula C₁₆H₂₉N₃O₆S

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 158.8
  • −1 ≤ LogP ≤ 5 0.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 391.5
  • LogP ≤ 5 0.18
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 158.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
InChI 
InChI=1S/C16H29N3O6S/c1-2-3-4-5-8-26-10-12(15(23)18-9-14(21)22)19-13(20)7-6-11(17)16(24)25/h11-12H,2-10,17H2,1H3,(H,18,23)(H,19,20)(H,21,22)(H,24,25)/t11-,12-/m0/s1
InChIKey 
HXJDWCWJDCOHDG-RYUDHWBXSA-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)