Ligand profile

ZINC100655906

Virtual-screening candidate from ZINC.

Bound to: KP13_05461 — Periplasmic murein peptide-binding protein

Via homolog UniProt Q7VL18 Formula C₁₂H₂₁NO₉
Tanimoto 0.78
Mol. weight 323.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC100655906
UniProt (similar protein)
Q7VL18
Tanimoto
0.783
Target protein
KP13_05461

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 323.30 Da
LogP (Crippen) -3.78
H-bond donors 6
H-bond acceptors 9
TPSA 165.78 Ų
Rotatable bonds 5
Aromatic rings 0 / 1
Heavy atoms 22
Fraction sp³ C 0.83
Formula C₁₂H₂₁NO₉

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 165.8
  • −1 ≤ LogP ≤ 5 -3.78
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 323.3
  • LogP ≤ 5 -3.78
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 165.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COC(=O)[C@]1(O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@H](O)[C@@H](O)CO)O1
InChI 
InChI=1S/C12H21NO9/c1-5(15)13-8-6(16)3-12(20,11(19)21-2)22-10(8)9(18)7(17)4-14/h6-10,14,16-18,20H,3-4H2,1-2H3,(H,13,15)/t6-,7-,8-,9+,10+,12-/m0/s1
InChIKey 
BKZQMWNJESHHSA-JQLBFFPPSA-N

Provenance

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

Method
LigQ nearest_k
Query
SLB
Homolog
Q7VL18

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_05461.

PDB 21

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)