Ligand profile

A5X

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

Bound to: KP13_02899 — Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit beta

Via homolog PDB 6cfo UniProt P11177 Formula C₁₄H₂₄N₄O₁₀P₃S⁺
Mol. weight 533.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A5X
PDB
6cfo
UniProt (similar protein)
P11177
Target protein
KP13_02899

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 533.35 Da
LogP (Crippen) 0.47
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 0.50
Formula C₁₄H₂₄N₄O₁₀P₃S⁺

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 0.47
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 533.4
  • LogP ≤ 5 0.47
  • 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)(O)P(=O)O)CCOP(=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C14H23N4O10P3S/c1-8-11(4-5-27-31(25,26)28-30(22,23)24)32-13(14(3,19)29(20)21)18(8)7-10-6-16-9(2)17-12(10)15/h6,19,29H,4-5,7H2,1-3H3,(H5-,15,16,17,20,21,22,23,24,25,26)/p+1/t14-/m0/s1
InChIKey 
CAOFPOCACDCAFN-AWEZNQCLSA-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
PF00676' '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_02899.

PDB 7

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

Ligand PDB entry

ZINC 13

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

Compound Similarity (Tanimoto)