Ligand profile

HKS

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

Bound to: KP13_04589 — Coenzyme PQQ synthesis protein B

Via homolog PDB 6e13 UniProt Q88QV5 Formula C₁₂H₁₆N₂O₆S
Mol. weight 316.34 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
HKS
PDB
6e13
UniProt (similar protein)
Q88QV5
Target protein
KP13_04589

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 316.34 Da
LogP (Crippen) -0.44
H-bond donors 6
H-bond acceptors 7
TPSA 167.10 Ų
Rotatable bonds 7
Aromatic rings 1 / 1
Heavy atoms 21
Fraction sp³ C 0.33
Formula C₁₂H₁₆N₂O₆S

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 167.1
  • −1 ≤ LogP ≤ 5 -0.44
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 316.3
  • LogP ≤ 5 -0.44
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 167.1
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(cc(c(c1O)O)SC[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
InChI 
InChI=1S/C12H16N2O6S/c13-6(11(17)18)1-5-2-8(15)10(16)9(3-5)21-4-7(14)12(19)20/h2-3,6-7,15-16H,1,4,13-14H2,(H,17,18)(H,19,20)/t6-,7+/m0/s1
InChIKey 
SXISMOAILJWTID-NKWVEPMBSA-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
PF12706

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_04589.

PDB 1

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

Ligand PDB entry

ZINC 36

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

Compound Similarity (Tanimoto)