Ligand profile

ZINC1529745

Virtual-screening candidate from ZINC.

Bound to: KP13_03421 — Glycerol kinase

Via homolog UniProt D3KVM3 Formula C₁₂H₉N₂O₈P
Tanimoto 0.79
Mol. weight 340.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1529745
UniProt (similar protein)
D3KVM3
Tanimoto
0.786
Target protein
KP13_03421

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 340.18 Da
LogP (Crippen) 3.06
H-bond donors 1
H-bond acceptors 7
TPSA 142.04 Ų
Rotatable bonds 6
Aromatic rings 2 / 2
Heavy atoms 23
Fraction sp³ C 0.00
Formula C₁₂H₉N₂O₈P

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 142.0
  • −1 ≤ LogP ≤ 5 3.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 340.2
  • LogP ≤ 5 3.06
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 142.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=[N+]([O-])c1ccc(OP(=O)(O)Oc2ccc([N+](=O)[O-])cc2)cc1
InChI 
InChI=1S/C12H9N2O8P/c15-13(16)9-1-5-11(6-2-9)21-23(19,20)22-12-7-3-10(4-8-12)14(17)18/h1-8H,(H,19,20)
InChIKey 
MHSVUSZEHNVFKW-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
4NP
Homolog
D3KVM3

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_03421.

PDB 13

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)