Ligand profile

ZINC13588928

Virtual-screening candidate from ZINC.

Bound to: KP13_00629 — DNA polymerase I

Via homolog UniProt P52026 Formula C₈H₁₄N₃O₁₂P₃S
Tanimoto 0.71
Mol. weight 469.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13588928
UniProt (similar protein)
P52026
Tanimoto
0.712
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 469.20 Da
LogP (Crippen) -0.24
H-bond donors 5
H-bond acceptors 12
TPSA 229.96 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 27
Fraction sp³ C 0.50
Formula C₈H₁₄N₃O₁₂P₃S

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 230.0
  • −1 ≤ LogP ≤ 5 -0.24
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 469.2
  • LogP ≤ 5 -0.24
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 230.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ccn([C@@H]2CS[C@H](CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O2)c(=O)n1
InChI 
InChI=1S/C8H14N3O12P3S/c9-5-1-2-11(8(12)10-5)6-4-27-7(21-6)3-20-25(16,17)23-26(18,19)22-24(13,14)15/h1-2,6-7H,3-4H2,(H,16,17)(H,18,19)(H2,9,10,12)(H2,13,14,15)/t6-,7+/m0/s1
InChIKey 
YLEQMGZZMCJKCN-NKWVEPMBSA-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)