Ligand profile

NDQ

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

Bound to: KP13_32378 — transketolase 2

Via homolog PDB 6tj8 UniProt P27302 Formula C₁₂H₁₉N₄O₈P₂S⁺
Mol. weight 441.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NDQ
PDB
6tj8
UniProt (similar protein)
P27302
Target protein
KP13_32378

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 441.32 Da
LogP (Crippen) 0.54
H-bond donors 4
H-bond acceptors 9
TPSA 178.20 Ų
Rotatable bonds 9
Aromatic rings 2 / 2
Heavy atoms 27
Fraction sp³ C 0.42
Formula C₁₂H₁₉N₄O₈P₂S⁺

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 178.2
  • −1 ≤ LogP ≤ 5 0.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 441.3
  • LogP ≤ 5 0.54
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 178.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc[n+]1Cc2cnc(nc2N)OC)CCOP(=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C12H18N4O8P2S/c1-8-10(3-4-23-26(20,21)24-25(17,18)19)27-7-16(8)6-9-5-14-12(22-2)15-11(9)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKey 
PWBCVHDHRGCQHM-UHFFFAOYSA-O

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_32378.

PDB 23

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)