Ligand profile

N5P

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 3t3f UniProt P19821 Formula C₁₃H₁₇N₂O₁₄P₃
Mol. weight 518.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
N5P
PDB
3t3f
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 518.20 Da
LogP (Crippen) 1.54
H-bond donors 5
H-bond acceptors 11
TPSA 237.35 Ų
Rotatable bonds 9
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.38
Formula C₁₃H₁₇N₂O₁₄P₃

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 237.3
  • −1 ≤ LogP ≤ 5 1.54
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 518.2
  • LogP ≤ 5 1.54
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 237.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)cc1[N+](=O)[O-]
InChI 
InChI=1S/C13H17N2O14P3/c16-11-6-13(14-4-3-8-5-9(15(17)18)1-2-10(8)14)27-12(11)7-26-31(22,23)29-32(24,25)28-30(19,20)21/h1-5,11-13,16H,6-7H2,(H,22,23)(H,24,25)(H2,19,20,21)
InChIKey 
JJJBDAFRCKSXDR-UHFFFAOYSA-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)