Ligand profile

0L5

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 4dfk UniProt P19821 Formula C₂₄H₄₀N₃O₁₆P₃
Mol. weight 719.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
0L5
PDB
4dfk
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 719.51 Da
LogP (Crippen) 0.89
H-bond donors 8
H-bond acceptors 13
TPSA 293.47 Ų
Rotatable bonds 20
Aromatic rings 1 / 2
Heavy atoms 46
Fraction sp³ C 0.71
Formula C₂₄H₄₀N₃O₁₆P₃

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 293.5
  • −1 ≤ LogP ≤ 5 0.89
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 719.5
  • LogP ≤ 5 0.89
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 293.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1C(C(OC1N2C=C(C(=O)NC2=O)C#CCCCNC(=O)CCCCCCCCCO)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C24H40N3O16P3/c28-14-10-5-3-1-2-4-8-12-21(30)25-13-9-6-7-11-18-16-27(24(32)26-23(18)31)22-15-19(29)20(41-22)17-40-45(36,37)43-46(38,39)42-44(33,34)35/h16,19-20,22,28-29H,1-6,8-10,12-15,17H2,(H,25,30)(H,36,37)(H,38,39)(H,26,31,32)(H2,33,34,35)
InChIKey 
UGHLPDROZCTFGX-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)