Ligand profile

0L3

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 4df4 UniProt P19821 Formula C₂₆H₄₂N₅O₁₄P₃
Mol. weight 741.56 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
0L3
PDB
4df4
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 741.56 Da
LogP (Crippen) 2.37
H-bond donors 8
H-bond acceptors 14
TPSA 295.34 Ų
Rotatable bonds 20
Aromatic rings 2 / 3
Heavy atoms 48
Fraction sp³ C 0.65
Formula C₂₆H₄₂N₅O₁₄P₃

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 295.3
  • −1 ≤ LogP ≤ 5 2.37
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 741.6
  • LogP ≤ 5 2.37
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 295.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c2c(ncnc2n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N)C#CCCCNC(=O)CCCCCCCCCO
InChI 
InChI=1S/C26H42N5O14P3/c27-25-24-19(11-7-6-9-13-28-22(34)12-8-4-2-1-3-5-10-14-32)16-31(26(24)30-18-29-25)23-15-20(33)21(43-23)17-42-47(38,39)45-48(40,41)44-46(35,36)37/h16,18,20-21,23,32-33H,1-6,8-10,12-15,17H2,(H,28,34)(H,38,39)(H,40,41)(H2,27,29,30)(H2,35,36,37)
InChIKey 
JQTQPUSSMXPQMW-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00476

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 34

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)