Ligand profile

TDX

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

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

Via homolog PDB 1kep UniProt Q8GIP9 Formula C₁₅H₂₄N₂O₁₅P₂
Mol. weight 534.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TDX
PDB
1kep
UniProt (similar protein)
Q8GIP9
Target protein
KP13_31530

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 534.30 Da
LogP (Crippen) -2.82
H-bond donors 7
H-bond acceptors 14
TPSA 256.53 Ų
Rotatable bonds 8
Aromatic rings 1 / 3
Heavy atoms 34
Fraction sp³ C 0.73
Formula C₁₅H₂₄N₂O₁₅P₂

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 256.5
  • −1 ≤ LogP ≤ 5 -2.82
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 534.3
  • LogP ≤ 5 -2.82
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 256.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O
InChI 
InChI=1S/C15H24N2O15P2/c1-6-3-17(15(23)16-13(6)22)10-2-7(18)9(30-10)5-29-33(24,25)32-34(26,27)31-14-12(21)11(20)8(19)4-28-14/h3,7-12,14,18-21H,2,4-5H2,1H3,(H,24,25)(H,26,27)(H,16,22,23)/t7-,8+,9+,10+,11-,12+,14+/m0/s1
InChIKey 
AJUADKZRQSBUAK-KDGZBOQCSA-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
PF16363

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 2

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)