Ligand profile

ZINC4878481

Virtual-screening candidate from ZINC.

Bound to: KP13_03293 — Deoxyribodipyrimidine photo-lyase

Via homolog UniProt P05327 Formula C₁₆H₁₇N₃O₆
Tanimoto 0.76
Mol. weight 347.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4878481
UniProt (similar protein)
P05327
Tanimoto
0.765
Target protein
KP13_03293

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 347.33 Da
LogP (Crippen) -1.74
H-bond donors 5
H-bond acceptors 8
TPSA 148.67 Ų
Rotatable bonds 5
Aromatic rings 1 / 3
Heavy atoms 25
Fraction sp³ C 0.31
Formula C₁₆H₁₇N₃O₆

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 148.7
  • −1 ≤ LogP ≤ 5 -1.74
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 347.3
  • LogP ≤ 5 -1.74
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 148.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=c1nc2n(C[C@@H](O)[C@@H](O)[C@H](O)CO)c3ccccc3cc-2c(=O)[nH]1
InChI 
InChI=1S/C16H17N3O6/c20-7-12(22)13(23)11(21)6-19-10-4-2-1-3-8(10)5-9-14(19)17-16(25)18-15(9)24/h1-5,11-13,20-23H,6-7H2,(H,18,24,25)/t11-,12-,13-/m1/s1
InChIKey 
CGDDRQLFQWMDOQ-JHJVBQTASA-N

Provenance

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

Method
LigQ nearest_k
Query
HDF
Homolog
P05327

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_03293.

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)