Ligand profile

ZINC4804745

Virtual-screening candidate from ZINC.

Bound to: KP13_31530 — dTDP-D-glucose 4,6-dehydratase in cps region

Via homolog UniProt Q8GIP9 Formula C₁₁H₁₆N₂O₆
Tanimoto 0.60
Mol. weight 272.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4804745
UniProt (similar protein)
Q8GIP9
Tanimoto
0.597
Target protein
KP13_31530

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 272.26 Da
LogP (Crippen) -2.15
H-bond donors 4
H-bond acceptors 7
TPSA 124.78 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 19
Fraction sp³ C 0.64
Formula C₁₁H₁₆N₂O₆

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 124.8
  • −1 ≤ LogP ≤ 5 -2.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 272.3
  • LogP ≤ 5 -2.15
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 124.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cn([C@H]2C[C@@H](O)[C@H](O)[C@H](CO)O2)c(=O)[nH]c1=O
InChI 
InChI=1S/C11H16N2O6/c1-5-3-13(11(18)12-10(5)17)8-2-6(15)9(16)7(4-14)19-8/h3,6-9,14-16H,2,4H2,1H3,(H,12,17,18)/t6-,7+,8-,9+/m1/s1
InChIKey 
VVJYUAYZJAKGRQ-XAVMHZPKSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
DAU
Homolog
Q8GIP9

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_31530.

PDB 3

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)