Ligand profile

TDW

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

Bound to: KP13_03277 — 2-oxoglutarate dehydrogenase E1 component

Via homolog PDB 3zhv UniProt A0R2B1 Formula C₁₄H₂₃N₄O₈P₂S⁺
Mol. weight 469.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TDW
PDB
3zhv
UniProt (similar protein)
A0R2B1
Target protein
KP13_03277

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 469.37 Da
LogP (Crippen) 0.90
H-bond donors 5
H-bond acceptors 9
TPSA 189.20 Ų
Rotatable bonds 9
Aromatic rings 2 / 2
Heavy atoms 29
Fraction sp³ C 0.50
Formula C₁₄H₂₃N₄O₈P₂S⁺

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 189.2
  • −1 ≤ LogP ≤ 5 0.90
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 469.4
  • LogP ≤ 5 0.90
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 189.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](C)O)CCOP(=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C14H22N4O8P2S/c1-8-12(4-5-25-28(23,24)26-27(20,21)22)29-14(9(2)19)18(8)7-11-6-16-10(3)17-13(11)15/h6,9,19H,4-5,7H2,1-3H3,(H4-,15,16,17,20,21,22,23,24)/p+1/t9-/m0/s1
InChIKey 
RRUVJGASJONMDY-VIFPVBQESA-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
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_03277.

PDB 9

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)