Ligand profile

CHEMBL59451

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_1238 — exodeoxyribonuclease III

Via homolog UniProt P27695 Formula C₁₆H₁₈O₈
pchembl 6.50 ~316.2 nM
Mol. weight 338.31 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL59451
UniProt (similar protein)
P27695
pchembl
6.500 (~316.2 nM)
Target protein
VK055_1238

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 338.31 Da
LogP (Crippen) 1.88
H-bond donors 6
H-bond acceptors 8
TPSA 139.84 Ų
Rotatable bonds 5
Aromatic rings 2 / 2
Heavy atoms 24
Fraction sp³ C 0.25
Formula C₁₆H₁₈O₈

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 139.8
  • −1 ≤ LogP ≤ 5 1.88
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 338.3
  • LogP ≤ 5 1.88
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 139.8
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COCc1cc(O)c(O)c(O)c1-c1c(COC)cc(O)c(O)c1O
InChI 
InChI=1S/C16H18O8/c1-23-5-7-3-9(17)13(19)15(21)11(7)12-8(6-24-2)4-10(18)14(20)16(12)22/h3-4,17-22H,5-6H2,1-2H3
InChIKey 
NEBCAMAQXZIVRE-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
ChEMBL
Activity
Active
Binding sites
PF03372

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_1238.

PDB 1

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

Ligand PDB entry

ChEMBL 99

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)