Ligand profile

OK3

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

Bound to: VK055_1868 — penicillin-binding protein 6

Via homolog PDB 5j8x UniProt P0AEB2 Formula C₁₇H₁₈BN₂O₆⁻
Mol. weight 357.15 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
OK3
PDB
5j8x
UniProt (similar protein)
P0AEB2
Target protein
VK055_1868

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 357.15 Da
LogP (Crippen) 0.04
H-bond donors 5
H-bond acceptors 6
TPSA 142.11 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.18
Formula C₁₇H₁₈BN₂O₆⁻

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 142.1
  • −1 ≤ LogP ≤ 5 0.04
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 357.2
  • LogP ≤ 5 0.04
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 142.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[B-]1([C@H](Cc2cccc(c2O1)C(=O)O)NC(=O)c3ccc(cc3)CN)(O)O
InChI 
InChI=1S/C17H18BN2O6/c19-9-10-4-6-11(7-5-10)16(21)20-14-8-12-2-1-3-13(17(22)23)15(12)26-18(14,24)25/h1-7,14,24-25H,8-9,19H2,(H,20,21)(H,22,23)/q-1/t14-/m0/s1
InChIKey 
QLXKUYDHLJOWQG-AWEZNQCLSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00768' 'PF07943

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_1868.

PDB 14

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

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)