Ligand profile

ZINC169292613

Virtual-screening candidate from ZINC.

Bound to: KP13_00629 — DNA polymerase I

Via homolog UniProt P52026 Formula C₉H₁₅N₆O₁₂P₃
Tanimoto 0.75
Mol. weight 492.17 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC169292613
UniProt (similar protein)
P52026
Tanimoto
0.750
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 492.17 Da
LogP (Crippen) 0.14
H-bond donors 5
H-bond acceptors 12
TPSA 278.72 Ų
Rotatable bonds 9
Aromatic rings 1 / 2
Heavy atoms 30
Fraction sp³ C 0.56
Formula C₉H₁₅N₆O₁₂P₃

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 278.7
  • −1 ≤ LogP ≤ 5 0.14
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 492.2
  • LogP ≤ 5 0.14
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 278.7
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[N-]=[N+]=N[C@@H]1C[C@H](n2ccc(N)nc2=O)O[C@@H]1CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C9H15N6O12P3/c10-7-1-2-15(9(16)12-7)8-3-5(13-14-11)6(25-8)4-24-29(20,21)27-30(22,23)26-28(17,18)19/h1-2,5-6,8H,3-4H2,(H,20,21)(H,22,23)(H2,10,12,16)(H2,17,18,19)/t5-,6-,8-/m1/s1
InChIKey 
KTLCZHWMPHUXRA-ATRFCDNQSA-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)