Ligand profile

SSJ

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 3oju UniProt P19821 Formula C₁₉H₂₈N₃O₁₅P₃
Mol. weight 631.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SSJ
PDB
3oju
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 631.36 Da
LogP (Crippen) 0.07
H-bond donors 7
H-bond acceptors 13
TPSA 267.61 Ų
Rotatable bonds 8
Aromatic rings 1 / 3
Heavy atoms 40
Fraction sp³ C 0.58
Formula C₁₉H₂₈N₃O₁₅P₃

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 267.6
  • −1 ≤ LogP ≤ 5 0.07
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 631.4
  • LogP ≤ 5 0.07
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 267.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1(C=C(C(N1O)(C)C)C#CC2=CN(C(=O)NC2=O)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)C
InChI 
InChI=1S/C19H28N3O15P3/c1-18(2)8-12(19(3,4)22(18)26)6-5-11-9-21(17(25)20-16(11)24)15-7-13(23)14(35-15)10-34-39(30,31)37-40(32,33)36-38(27,28)29/h8-9,13-15,23,26H,7,10H2,1-4H3,(H,30,31)(H,32,33)(H,20,24,25)(H2,27,28,29)
InChIKey 
GHJOELBEPYPBAG-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)