Ligand profile

ZINC142514175

Virtual-screening candidate from ZINC.

Bound to: KP13_00629 — DNA polymerase I

Via homolog UniProt P52026 Formula C₉H₁₆N₃O₁₂P₃S
Tanimoto 0.82
Mol. weight 483.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC142514175
UniProt (similar protein)
P52026
Tanimoto
0.818
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 483.23 Da
LogP (Crippen) 0.19
H-bond donors 6
H-bond acceptors 12
TPSA 233.12 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 28
Fraction sp³ C 0.56
Formula C₉H₁₆N₃O₁₂P₃S

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 233.1
  • −1 ≤ LogP ≤ 5 0.19
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 483.2
  • LogP ≤ 5 0.19
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 233.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ccn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O2)c(=S)n1
InChI 
InChI=1S/C9H16N3O12P3S/c10-7-1-2-12(9(28)11-7)8-3-5(13)6(22-8)4-21-26(17,18)24-27(19,20)23-25(14,15)16/h1-2,5-6,8,13H,3-4H2,(H,17,18)(H,19,20)(H2,10,11,28)(H2,14,15,16)/t5-,6-,8-/m0/s1
InChIKey 
VCHURPMMWRACNQ-HAFWLYHUSA-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)