Ligand profile

BMR

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 4c8k UniProt P19821 Formula C₁₆H₂₁O₁₃P₃
Mol. weight 514.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BMR
PDB
4c8k
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 514.25 Da
LogP (Crippen) 2.38
H-bond donors 5
H-bond acceptors 9
TPSA 198.51 Ų
Rotatable bonds 9
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.38
Formula C₁₆H₂₁O₁₃P₃

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 198.5
  • −1 ≤ LogP ≤ 5 2.38
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 514.3
  • LogP ≤ 5 2.38
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 198.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cc2ccccc2cc1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C16H21O13P3/c1-25-14-7-11-5-3-2-4-10(11)6-12(14)15-8-13(17)16(27-15)9-26-31(21,22)29-32(23,24)28-30(18,19)20/h2-7,13,15-17H,8-9H2,1H3,(H,21,22)(H,23,24)(H2,18,19,20)/t13-,15+,16+/m0/s1
InChIKey 
OYLYLYUMXXAEFZ-NUEKZKHPSA-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)