Ligand profile

5PN

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

Bound to: KP13_05543 — putative lactonase

Via homolog PDB 4keq UniProt Q988B9 Formula C₈H₇NO₃
Mol. weight 165.15 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5PN
PDB
4keq
UniProt (similar protein)
Q988B9
Target protein
KP13_05543

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 165.15 Da
LogP (Crippen) 0.77
H-bond donors 1
H-bond acceptors 4
TPSA 59.42 Ų
Rotatable bonds 0
Aromatic rings 1 / 2
Heavy atoms 12
Fraction sp³ C 0.25
Formula C₈H₇NO₃

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 59.4
  • −1 ≤ LogP ≤ 5 0.77
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 165.1
  • LogP ≤ 5 0.77
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 59.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c2c(cn1)C(=O)OC2)O
InChI 
InChI=1S/C8H7NO3/c1-4-7(10)6-3-12-8(11)5(6)2-9-4/h2,10H,3H2,1H3
InChIKey 
PPAXBSPBIWBREI-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
PF00753

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_05543.

PDB 7

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)