Ligand profile

N1T

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

Bound to: KP13_04322 — putative transketolase family protein

Via homolog PDB 1tkb UniProt P23254 Formula C₁₃H₁₉N₃O₇P₂S
Mol. weight 423.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
N1T
PDB
1tkb
UniProt (similar protein)
P23254
Target protein
KP13_04322

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 423.32 Da
LogP (Crippen) 0.81
H-bond donors 3
H-bond acceptors 8
TPSA 158.91 Ų
Rotatable bonds 8
Aromatic rings 2 / 2
Heavy atoms 26
Fraction sp³ C 0.38
Formula C₁₃H₁₉N₃O₇P₂S

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 158.9
  • −1 ≤ LogP ≤ 5 0.81
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 423.3
  • LogP ≤ 5 0.81
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 158.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc(c(n1)N)C[n+]2csc(c2C)CCO[P@](=O)(O)O[P@@](=O)(O)[O-]
InChI 
InChI=1S/C13H19N3O7P2S/c1-9-3-4-11(13(14)15-9)7-16-8-26-12(10(16)2)5-6-22-25(20,21)23-24(17,18)19/h3-4,8H,5-7H2,1-2H3,(H4-,14,15,17,18,19,20,21)
InChIKey 
JHNXLHRDUXBCJW-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
PF00456' 'PF02779

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_04322.

PDB 12

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 30

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)