Ligand profile

ZINC4545906

Virtual-screening candidate from ZINC.

Bound to: KP13_02520 — Lipoprotein nlpD

Via homolog UniProt O33599 Formula C₁₀H₁₇N₅O₆
Tanimoto 0.55
Mol. weight 303.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4545906
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 303.28 Da
LogP (Crippen) -4.51
H-bond donors 6
H-bond acceptors 6
TPSA 179.72 Ų
Rotatable bonds 9
Aromatic rings 0 / 0
Heavy atoms 21
Fraction sp³ C 0.50
Formula C₁₀H₁₇N₅O₆

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 179.7
  • −1 ≤ LogP ≤ 5 -4.51
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 303.3
  • LogP ≤ 5 -4.51
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 179.7
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)O
InChI 
InChI=1S/C10H17N5O6/c11-1-6(16)12-2-7(17)13-3-8(18)14-4-9(19)15-5-10(20)21/h1-5,11H2,(H,12,16)(H,13,17)(H,14,18)(H,15,19)(H,20,21)
InChIKey 
MXHCPCSDRGLRER-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)