Ligand profile

ZINC16887664

Virtual-screening candidate from ZINC.

Bound to: VK055_0258 — periplasmic oligopeptide-binding protein

Via homolog UniProt P33590 Formula C₉H₁₄O₆
Tanimoto 0.62
Mol. weight 218.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC16887664
UniProt (similar protein)
P33590
Tanimoto
0.625
Target protein
VK055_0258

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 218.20 Da
LogP (Crippen) 0.81
H-bond donors 3
H-bond acceptors 3
TPSA 111.90 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 15
Fraction sp³ C 0.67
Formula C₉H₁₄O₆

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 111.9
  • −1 ≤ LogP ≤ 5 0.81
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 218.2
  • LogP ≤ 5 0.81
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 111.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)CCC[C@@H](CCC(=O)O)C(=O)O
InChI 
InChI=1S/C9H14O6/c10-7(11)3-1-2-6(9(14)15)4-5-8(12)13/h6H,1-5H2,(H,10,11)(H,12,13)(H,14,15)/t6-/m0/s1
InChIKey 
YSARBTHSZMNCIB-LURJTMIESA-N

Provenance

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

Method
LigQ nearest_k
Query
HCT
Homolog
P33590

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_0258.

PDB 19

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)