Ligand profile

ZINC3900908

Virtual-screening candidate from ZINC.

Bound to: VK055_2111 — bacterial regulatory, gntR family protein

Via homolog UniProt Q8N5Z0 Formula C₂₁H₁₅NO₄
Tanimoto 0.66
Mol. weight 345.35 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3900908
UniProt (similar protein)
Q8N5Z0
Tanimoto
0.659
Target protein
VK055_2111

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 345.35 Da
LogP (Crippen) 3.13
H-bond donors 1
H-bond acceptors 3
TPSA 74.68 Ų
Rotatable bonds 4
Aromatic rings 3 / 4
Heavy atoms 26
Fraction sp³ C 0.10
Formula C₂₁H₁₅NO₄

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 74.7
  • −1 ≤ LogP ≤ 5 3.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 345.4
  • LogP ≤ 5 3.13
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 74.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)[C@@H](Cc1ccccc1)N1C(=O)c2cccc3cccc(c23)C1=O
InChI 
InChI=1S/C21H15NO4/c23-19-15-10-4-8-14-9-5-11-16(18(14)15)20(24)22(19)17(21(25)26)12-13-6-2-1-3-7-13/h1-11,17H,12H2,(H,25,26)/t17-/m1/s1
InChIKey 
SJGFGXSJCPZIMK-QGZVFWFLSA-N

Provenance

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

Method
LigQ nearest_k
Query
CHEMBL5429250
Homolog
Q8N5Z0

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_2111.

PDB 21

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 49

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

Compound Similarity (Tanimoto)