Ligand profile

HXZ

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 3m8r UniProt P19821 Formula C₁₂H₂₁N₂O₁₄P₃
Mol. weight 510.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HXZ
PDB
3m8r
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 510.22 Da
LogP (Crippen) -0.38
H-bond donors 6
H-bond acceptors 11
TPSA 244.14 Ų
Rotatable bonds 9
Aromatic rings 1 / 2
Heavy atoms 31
Fraction sp³ C 0.67
Formula C₁₂H₂₁N₂O₁₄P₃

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 -0.38
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 510.2
  • LogP ≤ 5 -0.38
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 244.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@]1([C@H](C[C@@H](O1)N2C=C(C(=O)NC2=O)C)O)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C12H21N2O14P3/c1-3-12(6-25-30(21,22)28-31(23,24)27-29(18,19)20)8(15)4-9(26-12)14-5-7(2)10(16)13-11(14)17/h5,8-9,15H,3-4,6H2,1-2H3,(H,21,22)(H,23,24)(H,13,16,17)(H2,18,19,20)/t8-,9+,12+/m0/s1
InChIKey 
RICQFQMPHJAPNN-YGOYTEALSA-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)