Ligand profile

AF

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 1ua1 UniProt P52026 Formula C₁₃H₁₁N
Mol. weight 181.24 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AF
PDB
1ua1
UniProt (similar protein)
P52026
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 181.24 Da
LogP (Crippen) 2.84
H-bond donors 1
H-bond acceptors 1
TPSA 26.02 Ų
Rotatable bonds 0
Aromatic rings 2 / 3
Heavy atoms 14
Fraction sp³ C 0.08
Formula C₁₃H₁₁N

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 26.0
  • −1 ≤ LogP ≤ 5 2.84
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 181.2
  • LogP ≤ 5 2.84
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 26.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc-2c(c1)Cc3c2ccc(c3)N
InChI 
InChI=1S/C13H11N/c14-11-5-6-13-10(8-11)7-9-3-1-2-4-12(9)13/h1-6,8H,7,14H2
InChIKey 
CFRFHWQYWJMEJN-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
PF00476

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_00629.

PDB 34

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)