Ligand profile

ZINC2561009

Virtual-screening candidate from ZINC.

Bound to: KP13_02520 — Lipoprotein nlpD

Via homolog UniProt O33599 Formula C₇H₁₃N₃O₄
Tanimoto 0.57
Mol. weight 203.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2561009
UniProt (similar protein)
O33599
Tanimoto
0.571
Target protein
KP13_02520

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 203.20 Da
LogP (Crippen) -2.35
H-bond donors 4
H-bond acceptors 4
TPSA 121.52 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 0.57
Formula C₇H₁₃N₃O₄

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 121.5
  • −1 ≤ LogP ≤ 5 -2.35
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 203.2
  • LogP ≤ 5 -2.35
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 121.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NCC(=O)NCCC(=O)NCC(=O)O
InChI 
InChI=1S/C7H13N3O4/c8-3-6(12)9-2-1-5(11)10-4-7(13)14/h1-4,8H2,(H,9,12)(H,10,11)(H,13,14)
InChIKey 
YYFOFHHIXIEANM-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
4SQ
Homolog
O33599

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_02520.

PDB 3

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

Ligand PDB entry

ZINC 18

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)