Ligand profile

A5J

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 5w6k UniProt P19821 Formula C₁₀H₁₈N₃O₁₅P₃
Mol. weight 513.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A5J
PDB
5w6k
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 513.18 Da
LogP (Crippen) -0.51
H-bond donors 9
H-bond acceptors 14
TPSA 292.12 Ų
Rotatable bonds 9
Aromatic rings 1 / 2
Heavy atoms 31
Fraction sp³ C 0.50
Formula C₁₀H₁₈N₃O₁₅P₃

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 292.1
  • −1 ≤ LogP ≤ 5 -0.51
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 513.2
  • LogP ≤ 5 -0.51
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 292.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c(nc(c1N(O)O)N)O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C10H18N3O15P3/c11-9-5(13(16)17)1-4(10(15)12-9)7-2-6(14)8(26-7)3-25-30(21,22)28-31(23,24)27-29(18,19)20/h1,6-8,14,16-17H,2-3H2,(H,21,22)(H,23,24)(H3,11,12,15)(H2,18,19,20)/t6-,7+,8+/m0/s1
InChIKey 
KAFFDRNDCIZAAZ-XLPZGREQSA-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)