Ligand profile

ZINC218114467

Virtual-screening candidate from ZINC.

Bound to: KP13_00629 — DNA polymerase I

Via homolog UniProt P52026 Formula C₉H₁₆N₃O₁₃P₃
Tanimoto 0.72
Mol. weight 467.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC218114467
UniProt (similar protein)
P52026
Tanimoto
0.724
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 467.16 Da
LogP (Crippen) -1.18
H-bond donors 6
H-bond acceptors 12
TPSA 250.19 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 28
Fraction sp³ C 0.56
Formula C₉H₁₆N₃O₁₃P₃

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 250.2
  • −1 ≤ LogP ≤ 5 -1.18
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 467.2
  • LogP ≤ 5 -1.18
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 250.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)C[C@@H]2O)c(=O)n1
InChI 
InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-6(13)3-5(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6-,8+/m0/s1
InChIKey 
CHKFLBOLYREYDO-VMHSAVOQSA-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)