Ligand profile

3FL

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

Bound to: KP13_00801 — Uracil-DNA glycosylase

Via homolog PDB 3fcl UniProt P13051 Formula C₁₇H₂₂N₄O₄
Mol. weight 346.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3FL
PDB
3fcl
UniProt (similar protein)
P13051
Target protein
KP13_00801

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 346.39 Da
LogP (Crippen) 0.42
H-bond donors 5
H-bond acceptors 5
TPSA 127.08 Ų
Rotatable bonds 10
Aromatic rings 2 / 2
Heavy atoms 25
Fraction sp³ C 0.35
Formula C₁₇H₂₂N₄O₄

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 127.1
  • −1 ≤ LogP ≤ 5 0.42
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 346.4
  • LogP ≤ 5 0.42
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 127.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc(c1)C(=O)O)CNCCCCNCC2=CC(=O)NC(=O)N2
InChI 
InChI=1S/C17H22N4O4/c22-15-9-14(20-17(25)21-15)11-19-7-2-1-6-18-10-12-4-3-5-13(8-12)16(23)24/h3-5,8-9,18-19H,1-2,6-7,10-11H2,(H,23,24)(H2,20,21,22,25)
InChIKey 
PLKKHOGCWCJFJX-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
PF03167

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_00801.

PDB 15

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

Ligand PDB entry

ChEMBL 1

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)