Ligand profile

ZINC12428290

Virtual-screening candidate from ZINC.

Bound to: KP13_04589 — Coenzyme PQQ synthesis protein B

Via homolog UniProt Q88QV5 Formula C₉H₉N₃O₇
Tanimoto 0.50
Mol. weight 271.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12428290
UniProt (similar protein)
Q88QV5
Tanimoto
0.500
Target protein
KP13_04589

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 271.18 Da
LogP (Crippen) 0.16
H-bond donors 3
H-bond acceptors 7
TPSA 169.83 Ų
Rotatable bonds 5
Aromatic rings 1 / 1
Heavy atoms 19
Fraction sp³ C 0.22
Formula C₉H₉N₃O₇

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 169.8
  • −1 ≤ LogP ≤ 5 0.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 271.2
  • LogP ≤ 5 0.16
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 169.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@@H](Cc1cc([N+](=O)[O-])c(O)c([N+](=O)[O-])c1)C(=O)O
InChI 
InChI=1S/C9H9N3O7/c10-5(9(14)15)1-4-2-6(11(16)17)8(13)7(3-4)12(18)19/h2-3,5,13H,1,10H2,(H,14,15)/t5-/m0/s1
InChIKey 
SAZOSDSFLRXREA-YFKPBYRVSA-N

Provenance

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

Method
LigQ nearest_k
Query
HKS
Homolog
Q88QV5

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_04589.

PDB 2

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

Ligand PDB entry

ZINC 35

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

Compound Similarity (Tanimoto)