Ligand profile

O2T

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

Bound to: KP13_05584 — putative pyruvate-flavodoxin oxidoreductase

Via homolog PDB 5exd UniProt Q2RI41 Formula C₁₄H₂₀N₄O₁₁P₂S
Mol. weight 514.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
O2T
PDB
5exd
UniProt (similar protein)
Q2RI41
Target protein
KP13_05584

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 514.35 Da
LogP (Crippen) -1.57
H-bond donors 6
H-bond acceptors 12
TPSA 249.56 Ų
Rotatable bonds 10
Aromatic rings 2 / 2
Heavy atoms 32
Fraction sp³ C 0.43
Formula C₁₄H₂₀N₄O₁₁P₂S

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 249.6
  • −1 ≤ LogP ≤ 5 -1.57
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 514.3
  • LogP ≤ 5 -1.57
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 249.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C(=O)O)(O)O)CCOP(=O)(O)OP(=O)(O)[O-]
InChI 
InChI=1S/C14H20N4O11P2S/c1-7-10(3-4-28-31(26,27)29-30(23,24)25)32-12(14(21,22)13(19)20)18(7)6-9-5-16-8(2)17-11(9)15/h5,21-22H,3-4,6H2,1-2H3,(H5-,15,16,17,19,20,23,24,25,26,27)
InChIKey 
DVVUFOVKVOOQQB-UHFFFAOYSA-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
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)