Ligand profile

3FI

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

Bound to: KP13_00801 — Uracil-DNA glycosylase

Via homolog PDB 3fci UniProt P13051 Formula C₁₆H₁₈N₄O₅
Mol. weight 346.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3FI
PDB
3fci
UniProt (similar protein)
P13051
Target protein
KP13_00801

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 346.34 Da
LogP (Crippen) 0.29
H-bond donors 4
H-bond acceptors 6
TPSA 136.64 Ų
Rotatable bonds 9
Aromatic rings 2 / 2
Heavy atoms 25
Fraction sp³ C 0.25
Formula C₁₆H₁₈N₄O₅

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 136.6
  • −1 ≤ LogP ≤ 5 0.29
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 346.3
  • LogP ≤ 5 0.29
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 136.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc(c1)C(=O)O)\C=N\OCCCNCC2=CC(=O)NC(=O)N2
InChI 
InChI=1S/C16H18N4O5/c21-14-8-13(19-16(24)20-14)10-17-5-2-6-25-18-9-11-3-1-4-12(7-11)15(22)23/h1,3-4,7-9,17H,2,5-6,10H2,(H,22,23)(H2,19,20,21,24)/b18-9+
InChIKey 
DNNMFLCWPRQYIC-GIJQJNRQSA-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)