Ligand profile

ZINC4545903

Virtual-screening candidate from ZINC.

Bound to: KP13_02520 — Lipoprotein nlpD

Via homolog UniProt O33599 Formula C₁₂H₂₀N₆O₇
Tanimoto 0.55
Mol. weight 360.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4545903
UniProt (similar protein)
O33599
Tanimoto
0.545
Target protein
KP13_02520

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 360.33 Da
LogP (Crippen) -5.39
H-bond donors 7
H-bond acceptors 7
TPSA 208.82 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 25
Fraction sp³ C 0.50
Formula C₁₂H₂₀N₆O₇

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 208.8
  • −1 ≤ LogP ≤ 5 -5.39
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 360.3
  • LogP ≤ 5 -5.39
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 208.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NCC(=O)NCC(=O)NCC(=O)NCC(=O)NCC(=O)NCC(=O)O
InChI 
InChI=1S/C12H20N6O7/c13-1-7(19)14-2-8(20)15-3-9(21)16-4-10(22)17-5-11(23)18-6-12(24)25/h1-6,13H2,(H,14,19)(H,15,20)(H,16,21)(H,17,22)(H,18,23)(H,24,25)
InChIKey 
XJFPXLWGZWAWRQ-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)