Ligand profile

TD6

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

Bound to: KP13_03277 — 2-oxoglutarate dehydrogenase E1 component

Via homolog PDB 3zhs UniProt A0R2B1 Formula C₁₆H₂₅N₄O₁₀P₂S⁺
Mol. weight 527.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TD6
PDB
3zhs
UniProt (similar protein)
A0R2B1
Target protein
KP13_03277

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 527.41 Da
LogP (Crippen) 0.74
H-bond donors 6
H-bond acceptors 10
TPSA 226.50 Ų
Rotatable bonds 12
Aromatic rings 2 / 2
Heavy atoms 33
Fraction sp³ C 0.50
Formula C₁₆H₂₅N₄O₁₀P₂S⁺

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 226.5
  • −1 ≤ LogP ≤ 5 0.74
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 527.4
  • LogP ≤ 5 0.74
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 226.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C16H24N4O10P2S/c1-9-13(5-6-29-32(27,28)30-31(24,25)26)33-16(12(21)3-4-14(22)23)20(9)8-11-7-18-10(2)19-15(11)17/h7,12,21H,3-6,8H2,1-2H3,(H5-,17,18,19,22,23,24,25,26,27,28)/p+1/t12-/m0/s1
InChIKey 
ZWUKRGPVMMTMAF-LBPRGKRZSA-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)