Ligand profile

NZI

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 5oxj UniProt P19821 Formula C₁₂H₁₇N₂O₁₃P₃
Mol. weight 490.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NZI
PDB
5oxj
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 490.19 Da
LogP (Crippen) 0.32
H-bond donors 6
H-bond acceptors 10
TPSA 227.07 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 30
Fraction sp³ C 0.42
Formula C₁₂H₁₇N₂O₁₃P₃

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 227.1
  • −1 ≤ LogP ≤ 5 0.32
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 490.2
  • LogP ≤ 5 0.32
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 227.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)NC(=O)N2[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C12H17N2O13P3/c15-9-5-11(14-8-4-2-1-3-7(8)13-12(14)16)25-10(9)6-24-29(20,21)27-30(22,23)26-28(17,18)19/h1-4,9-11,15H,5-6H2,(H,13,16)(H,20,21)(H,22,23)(H2,17,18,19)/t9-,10+,11+/m0/s1
InChIKey 
OMCWLYQAPHJDBD-HBNTYKKESA-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)