Ligand profile

ZINC4353346

Virtual-screening candidate from ZINC.

Bound to: KP13_05136 — Riboflavin synthase alpha chain

Via homolog UniProt Q06877 Formula C₁₇H₂₀N₄O₆
Tanimoto 0.67
Mol. weight 376.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4353346
UniProt (similar protein)
Q06877
Tanimoto
0.673
Target protein
KP13_05136

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 376.37 Da
LogP (Crippen) -1.72
H-bond donors 5
H-bond acceptors 9
TPSA 161.56 Ų
Rotatable bonds 5
Aromatic rings 1 / 3
Heavy atoms 27
Fraction sp³ C 0.41
Formula C₁₇H₂₀N₄O₆

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 161.6
  • −1 ≤ LogP ≤ 5 -1.72
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 376.4
  • LogP ≤ 5 -1.72
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 161.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc2c(nc3c(=O)[nH]c(=O)nc-3n2C[C@H](O)[C@H](O)[C@H](O)CO)c1C
InChI 
InChI=1S/C17H20N4O6/c1-7-3-4-9-12(8(7)2)18-13-15(19-17(27)20-16(13)26)21(9)5-10(23)14(25)11(24)6-22/h3-4,10-11,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/t10-,11+,14-/m0/s1
InChIKey 
LXMDIEJPPQSFFB-WDMOLILDSA-N

Provenance

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

Method
LigQ nearest_k
Query
RBF
Homolog
Q06877

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_05136.

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)