Ligand profile

0KL

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 4dfj UniProt P19821 Formula C₁₄H₂₂N₃O₁₄P₃
Mol. weight 549.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
0KL
PDB
4dfj
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 549.26 Da
LogP (Crippen) -1.38
H-bond donors 7
H-bond acceptors 12
TPSA 270.16 Ų
Rotatable bonds 10
Aromatic rings 1 / 2
Heavy atoms 34
Fraction sp³ C 0.57
Formula C₁₄H₂₂N₃O₁₄P₃

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 270.2
  • −1 ≤ LogP ≤ 5 -1.38
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 549.3
  • LogP ≤ 5 -1.38
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 270.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1C(C(OC1N2C=C(C(=O)NC2=O)C#CCCCN)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C14H22N3O14P3/c15-5-3-1-2-4-9-7-17(14(20)16-13(9)19)12-6-10(18)11(29-12)8-28-33(24,25)31-34(26,27)30-32(21,22)23/h7,10-12,18H,1,3,5-6,8,15H2,(H,24,25)(H,26,27)(H,16,19,20)(H2,21,22,23)
InChIKey 
WENDCSLWIXFOST-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)