Ligand profile

O34

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

Bound to: KP13_04219 — ATP-binding/permease protein cydC

Via homolog PDB 6p6j UniProt Q1RAG3 Formula C₂₁H₂₇N₃O₄S₃
Mol. weight 481.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
O34
PDB
6p6j
UniProt (similar protein)
Q1RAG3
Target protein
KP13_04219

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 481.67 Da
LogP (Crippen) 2.66
H-bond donors 4
H-bond acceptors 9
TPSA 114.51 Ų
Rotatable bonds 6
Aromatic rings 1 / 4
Heavy atoms 31
Fraction sp³ C 0.57
Formula C₂₁H₂₇N₃O₄S₃

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 114.5
  • −1 ≤ LogP ≤ 5 2.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 481.7
  • LogP ≤ 5 2.66
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 114.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@]1(CSC(=N1)C(C)(C)[C@@H]([C@@H]2CS[C@@H](N2)[C@H]3CSC(=N3)c4ccccc4O)O)C(=O)O
InChI 
InChI=1S/C21H27N3O4S3/c1-20(2,18-24-21(3,10-31-18)19(27)28)15(26)12-8-30-17(22-12)13-9-29-16(23-13)11-6-4-5-7-14(11)25/h4-7,12-13,15,17,22,25-26H,8-10H2,1-3H3,(H,27,28)/t12-,13+,15+,17+,21+/m0/s1
InChIKey 
JHYVWAMMAMCUIR-NIJJZIDKSA-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
PF00664

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_04219.

PDB 3

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)