Ligand profile

54F

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

Bound to: KP13_03868 — 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

Via homolog PDB 4b0b UniProt O33877 Formula C₁₁H₁₀N₂O
Mol. weight 186.21 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
54F
PDB
4b0b
UniProt (similar protein)
O33877
Target protein
KP13_03868

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 186.21 Da
LogP (Crippen) 2.46
H-bond donors 1
H-bond acceptors 3
TPSA 48.14 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 14
Fraction sp³ C 0.00
Formula C₁₁H₁₀N₂O

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 48.1
  • −1 ≤ LogP ≤ 5 2.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 186.2
  • LogP ≤ 5 2.46
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 48.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccnc(c1)Oc2cccc(c2)N
InChI 
InChI=1S/C11H10N2O/c12-9-4-3-5-10(8-9)14-11-6-1-2-7-13-11/h1-8H,12H2
InChIKey 
CLQMOPKXIBQKKG-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
PF07977

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_03868.

PDB 12

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)