Ligand profile

ZINC142487928

Virtual-screening candidate from ZINC.

Bound to: KP13_00629 — DNA polymerase I

Via homolog UniProt P52026 Formula C₉H₁₆N₃O₁₄P₃
Tanimoto 0.72
Mol. weight 483.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC142487928
UniProt (similar protein)
P52026
Tanimoto
0.719
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 483.16 Da
LogP (Crippen) -1.48
H-bond donors 7
H-bond acceptors 13
TPSA 270.42 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 29
Fraction sp³ C 0.56
Formula C₉H₁₆N₃O₁₄P₃

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 270.4
  • −1 ≤ LogP ≤ 5 -1.48
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 483.2
  • LogP ≤ 5 -1.48
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 270.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc(=O)n([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O2)cc1O
InChI 
InChI=1S/C9H16N3O14P3/c10-8-5(14)2-12(9(15)11-8)7-1-4(13)6(24-7)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h2,4,6-7,13-14H,1,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-/m0/s1
InChIKey 
APWMGTRTGVBXNC-QTSITTDLSA-N

Provenance

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

Method
LigQ nearest_k
Query
DCP
Homolog
P52026

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_00629.

PDB 35

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)