Ligand profile

HXB

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 3m8s UniProt P19821 Formula C₁₁H₁₉N₂O₁₄P₃
Mol. weight 496.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HXB
PDB
3m8s
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 496.20 Da
LogP (Crippen) -0.77
H-bond donors 6
H-bond acceptors 11
TPSA 244.14 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 30
Fraction sp³ C 0.64
Formula C₁₁H₁₉N₂O₁₄P₃

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 244.1
  • −1 ≤ LogP ≤ 5 -0.77
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 496.2
  • LogP ≤ 5 -0.77
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 244.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@@](O2)(C)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C11H19N2O14P3/c1-6-4-13(10(16)12-9(6)15)8-3-7(14)11(2,25-8)5-24-29(20,21)27-30(22,23)26-28(17,18)19/h4,7-8,14H,3,5H2,1-2H3,(H,20,21)(H,22,23)(H,12,15,16)(H2,17,18,19)/t7-,8+,11+/m0/s1
InChIKey 
IUVOCYKHODEDJI-VAOFZXAKSA-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)