Ligand profile

TDO

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

Bound to: KP13_03795 — dTDP-4-dehydrorhamnose 3,5-epimerase in cps region

Via homolog PDB 6ndr UniProt Q5ZXH5 Formula C₁₆H₂₄N₂O₁₅P₂
Mol. weight 546.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TDO
PDB
6ndr
UniProt (similar protein)
Q5ZXH5
Target protein
KP13_03795

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 546.32 Da
LogP (Crippen) -2.22
H-bond donors 6
H-bond acceptors 14
TPSA 253.37 Ų
Rotatable bonds 8
Aromatic rings 1 / 3
Heavy atoms 35
Fraction sp³ C 0.69
Formula C₁₆H₂₄N₂O₁₅P₂

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 253.4
  • −1 ≤ LogP ≤ 5 -2.22
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 546.3
  • LogP ≤ 5 -2.22
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 253.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1C(=O)[C@H]([C@H]([C@H](O1)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)O
InChI 
InChI=1S/C16H24N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-10,12-13,15,19,21-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8-,9+,10+,12+,13+,15+/m0/s1
InChIKey 
PSXWNITXWWECNY-LPVGZGSHSA-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
PF00908

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_03795.

PDB 4

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

Ligand PDB entry

ChEMBL 5

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)