Ligand profile

3NP

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

Bound to: KP13_31481 — Fumarate reductase flavoprotein subunit

Via homolog PDB 3p4s UniProt P00363 Formula C₃H₅NO₄
Mol. weight 119.08 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3NP
PDB
3p4s
UniProt (similar protein)
P00363
Target protein
KP13_31481

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 119.08 Da
LogP (Crippen) -0.26
H-bond donors 1
H-bond acceptors 3
TPSA 80.44 Ų
Rotatable bonds 3
Aromatic rings 0 / 0
Heavy atoms 8
Fraction sp³ C 0.67
Formula C₃H₅NO₄

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 80.4
  • −1 ≤ LogP ≤ 5 -0.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 119.1
  • LogP ≤ 5 -0.26
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 80.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C[N+](=O)[O-])C(=O)O
InChI 
InChI=1S/C3H5NO4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)
InChIKey 
WBLZUCOIBUDNBV-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00890

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_31481.

PDB 35

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)