Ligand profile

B9X

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

Bound to: KP13_01945 — DNA polymerase II

Via homolog PDB 6ish UniProt Q56366 Formula C₁₇H₂₆N₅O₉P
Mol. weight 475.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B9X
PDB
6ish
UniProt (similar protein)
Q56366
Target protein
KP13_01945

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 475.40 Da
LogP (Crippen) 0.16
H-bond donors 3
H-bond acceptors 12
TPSA 190.37 Ų
Rotatable bonds 12
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.65
Formula C₁₇H₂₆N₅O₉P

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 190.4
  • −1 ≤ LogP ≤ 5 0.16
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 475.4
  • LogP ≤ 5 0.16
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 190.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCOCCOCCC(=O)O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n2cnc3c2ncnc3N
InChI 
InChI=1S/C17H26N5O9P/c1-2-27-5-6-28-4-3-14(23)31-11-7-13(30-12(11)8-29-32(24,25)26)22-10-21-15-16(18)19-9-20-17(15)22/h9-13H,2-8H2,1H3,(H2,18,19,20)(H2,24,25,26)/t11-,12+,13+/m0/s1
InChIKey 
YOZZSXDAZQISJN-YNEHKIRRSA-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
PF00136

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_01945.

PDB 13

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)