Ligand profile

TDL

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

Bound to: KP13_05584 — putative pyruvate-flavodoxin oxidoreductase

Via homolog PDB 6cio UniProt Q2RMD6 Formula C₁₅H₂₃N₄O₁₀P₂S⁺
Mol. weight 513.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TDL
PDB
6cio
UniProt (similar protein)
Q2RMD6
Target protein
KP13_05584

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 513.38 Da
LogP (Crippen) 0.13
H-bond donors 6
H-bond acceptors 10
TPSA 226.50 Ų
Rotatable bonds 10
Aromatic rings 2 / 2
Heavy atoms 32
Fraction sp³ C 0.47
Formula C₁₅H₂₃N₄O₁₀P₂S⁺

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 0.13
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 513.4
  • LogP ≤ 5 0.13
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • 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@](C)(C(=O)O)O)CCO[P@@](=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C15H22N4O10P2S/c1-8-11(4-5-28-31(26,27)29-30(23,24)25)32-13(15(3,22)14(20)21)19(8)7-10-6-17-9(2)18-12(10)16/h6,22H,4-5,7H2,1-3H3,(H5-,16,17,18,20,21,23,24,25,26,27)/p+1/t15-/m1/s1
InChIKey 
TVDSMGSBVYONNB-OAHLLOKOSA-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
PF01855' 'PF02775

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_05584.

PDB 5

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

Ligand PDB entry

ZINC 3

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)