Ligand profile

ZINC5030599

Virtual-screening candidate from ZINC.

Bound to: KP13_00190 — Lipopolysaccharide core biosynthesis glycosyltransferase waaE

Via homolog UniProt B7SY86 Formula C₁₀H₁₂N₈O₄
Tanimoto 0.68
Mol. weight 308.26 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5030599
UniProt (similar protein)
B7SY86
Tanimoto
0.678
Target protein
KP13_00190

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 308.26 Da
LogP (Crippen) -1.37
H-bond donors 4
H-bond acceptors 9
TPSA 188.04 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 22
Fraction sp³ C 0.50
Formula C₁₀H₁₂N₈O₄

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 188.0
  • −1 ≤ LogP ≤ 5 -1.37
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 308.3
  • LogP ≤ 5 -1.37
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 188.0
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[N-]=[N+]=NC[C@@H]1O[C@H](n2cnc3c(=O)[nH]c(N)nc32)[C@H](O)[C@@H]1O
InChI 
InChI=1S/C10H12N8O4/c11-10-15-7-4(8(21)16-10)13-2-18(7)9-6(20)5(19)3(22-9)1-14-17-12/h2-3,5-6,9,19-20H,1H2,(H3,11,15,16,21)/t3-,5+,6+,9-/m0/s1
InChIKey 
IURRXTYHKBREQT-PXMDKTAGSA-N

Provenance

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

Method
LigQ nearest_k
Query
5GP
Homolog
B7SY86

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_00190.

PDB 3

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)