Ligand profile

ZINC5542410

Virtual-screening candidate from ZINC.

Bound to: KP13_04750 — Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase

Via homolog UniProt Q05603 Formula C₁₂H₁₄N₂O₄
Tanimoto 0.66
Mol. weight 250.25 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5542410
UniProt (similar protein)
Q05603
Tanimoto
0.660
Target protein
KP13_04750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 250.25 Da
LogP (Crippen) -0.35
H-bond donors 3
H-bond acceptors 6
TPSA 87.74 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 18
Fraction sp³ C 0.42
Formula C₁₂H₁₄N₂O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 87.7
  • −1 ≤ LogP ≤ 5 -0.35
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 250.3
  • LogP ≤ 5 -0.35
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 87.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
OC[C@@H]1O[C@H](n2cnc3ccccc32)[C@@H](O)[C@@H]1O
InChI 
InChI=1S/C12H14N2O4/c15-5-9-10(16)11(17)12(18-9)14-6-13-7-3-1-2-4-8(7)14/h1-4,6,9-12,15-17H,5H2/t9-,10+,11-,12-/m0/s1
InChIKey 
VQJDOEMQZNKEMJ-USZNOCQGSA-N

Provenance

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

Method
LigQ nearest_k
Query
1RB
Homolog
Q05603

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_04750.

PDB 26

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)