Ligand profile

TD9

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

Bound to: KP13_03277 — 2-oxoglutarate dehydrogenase E1 component

Via homolog PDB 3zht UniProt A0R2B1 Formula C₁₇H₂₇N₄O₁₀P₂S⁺
Mol. weight 541.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TD9
PDB
3zht
UniProt (similar protein)
A0R2B1
Target protein
KP13_03277

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 541.44 Da
LogP (Crippen) 1.13
H-bond donors 6
H-bond acceptors 10
TPSA 226.50 Ų
Rotatable bonds 13
Aromatic rings 2 / 2
Heavy atoms 34
Fraction sp³ C 0.53
Formula C₁₇H₂₇N₄O₁₀P₂S⁺

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 1.13
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 541.4
  • LogP ≤ 5 1.13
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • 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](CCCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C17H26N4O10P2S/c1-10-14(6-7-30-33(28,29)31-32(25,26)27)34-17(13(22)4-3-5-15(23)24)21(10)9-12-8-19-11(2)20-16(12)18/h8,13,22H,3-7,9H2,1-2H3,(H5-,18,19,20,23,24,25,26,27,28,29)/p+1/t13-/m0/s1
InChIKey 
WMOBQHPEAJZBCW-ZDUSSCGKSA-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)