Ligand profile

CHEMBL3343825

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00978 — Menaquinone-specific isochorismate synthase

Via homolog UniProt Q9X9I8 Formula C₉H₄N₂O₉S
pchembl 6.10 ~794.3 nM
Mol. weight 316.20 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3343825
UniProt (similar protein)
Q9X9I8
pchembl
6.100 (~794.3 nM)
Target protein
KP13_00978

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 316.20 Da
LogP (Crippen) 1.82
H-bond donors 0
H-bond acceptors 10
TPSA 152.02 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 21
Fraction sp³ C 0.11
Formula C₉H₄N₂O₉S

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 152.0
  • −1 ≤ LogP ≤ 5 1.82
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 316.2
  • LogP ≤ 5 1.82
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 152.0
PAINS Alert

Matches PAINS filter: thio_carbonate_A(15). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COC(=O)Oc1c([N+](=O)[O-])cc2oc(=O)sc2c1[N+](=O)[O-]
InChI 
InChI=1S/C9H4N2O9S/c1-18-8(12)20-6-3(10(14)15)2-4-7(5(6)11(16)17)21-9(13)19-4/h2H,1H3
InChIKey 
BXVKBNPNUFOKOS-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
Binding sites
PF00425

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_00978.

PDB 6

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

Ligand PDB entry

ChEMBL 13

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)