Ligand profile

5SI

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 3sv3 UniProt P19821 Formula C₁₅H₂₀NO₁₂P₃S
Mol. weight 531.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5SI
PDB
3sv3
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 531.31 Da
LogP (Crippen) 2.67
H-bond donors 5
H-bond acceptors 10
TPSA 194.21 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.40
Formula C₁₅H₂₀NO₁₂P₃S

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 194.2
  • −1 ≤ LogP ≤ 5 2.67
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 531.3
  • LogP ≤ 5 2.67
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 194.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc2c(c1)C=CN(C2=S)[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C15H20NO12P3S/c1-9-2-3-11-10(6-9)4-5-16(15(11)32)14-7-12(17)13(26-14)8-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-6,12-14,17H,7-8H2,1H3,(H,21,22)(H,23,24)(H2,18,19,20)/t12-,13+,14+/m0/s1
InChIKey 
HHAKTXADNAZKDV-BFHYXJOUSA-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)