Ligand profile

N9N

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_3490 — phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase

Via homolog PDB 6thc UniProt A0QWT2 Formula C₁₃H₁₀O₅
Mol. weight 246.22 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
N9N
PDB
6thc
UniProt (similar protein)
A0QWT2
Target protein
VK055_3490

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 246.22 Da
LogP (Crippen) 1.74
H-bond donors 4
H-bond acceptors 5
TPSA 97.99 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 18
Fraction sp³ C 0.00
Formula C₁₃H₁₀O₅

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 98.0
  • −1 ≤ LogP ≤ 5 1.74
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 246.2
  • LogP ≤ 5 1.74
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 98.0
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 
c1cc(ccc1C(=O)c2ccc(c(c2O)O)O)O
InChI 
InChI=1S/C13H10O5/c14-8-3-1-7(2-4-8)11(16)9-5-6-10(15)13(18)12(9)17/h1-6,14-15,17-18H
InChIKey 
ZRDYULMDEGRWRC-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
PDB
Binding sites
PF04127

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_3490.

PDB 2

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)