Ligand profile

0L4

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 4df8 UniProt P19821 Formula C₁₆H₂₄N₅O₁₂P₃
Mol. weight 571.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
0L4
PDB
4df8
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 571.31 Da
LogP (Crippen) 0.10
H-bond donors 7
H-bond acceptors 13
TPSA 272.03 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 36
Fraction sp³ C 0.50
Formula C₁₆H₂₄N₅O₁₂P₃

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 272.0
  • −1 ≤ LogP ≤ 5 0.10
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 571.3
  • LogP ≤ 5 0.10
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 272.0
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#CCCCN
InChI 
InChI=1S/C16H24N5O12P3/c17-5-3-1-2-4-10-7-21(16-14(10)15(18)19-9-20-16)13-6-11(22)12(31-13)8-30-35(26,27)33-36(28,29)32-34(23,24)25/h7,9,11-13,22H,1,3,5-6,8,17H2,(H,26,27)(H,28,29)(H2,18,19,20)(H2,23,24,25)
InChIKey 
MCSGHAFVOBYWGE-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)