Ligand profile

XG4

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 6fbc UniProt P19821 Formula C₁₀H₁₇N₆O₁₂P₃
Mol. weight 506.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XG4
PDB
6fbc
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 506.20 Da
LogP (Crippen) -1.73
H-bond donors 8
H-bond acceptors 12
TPSA 281.67 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 31
Fraction sp³ C 0.50
Formula C₁₀H₁₇N₆O₁₂P₃

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 281.7
  • −1 ≤ LogP ≤ 5 -1.73
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 506.2
  • LogP ≤ 5 -1.73
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 281.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C10H17N6O12P3/c11-10-13-8-7(9(18)14-10)12-3-16(8)6-1-4(17)5(27-6)2-26-29(19,20)15-30(21,22)28-31(23,24)25/h3-6,17H,1-2H2,(H2,23,24,25)(H3,11,13,14,18)(H3,15,19,20,21,22)/t4-,5+,6+/m0/s1
InChIKey 
DWGAAFQEGIMTIA-KVQBGUIXSA-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)