Ligand profile

BO9

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

Bound to: VK055_1655 — penicillin-binding protein 6

Via homolog PDB 1z6f UniProt P0AEB2 Formula C₂₆H₄₁BN₄O₁₀
Mol. weight 580.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BO9
PDB
1z6f
UniProt (similar protein)
P0AEB2
Target protein
VK055_1655

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 580.44 Da
LogP (Crippen) 0.84
H-bond donors 7
H-bond acceptors 9
TPSA 212.62 Ų
Rotatable bonds 16
Aromatic rings 1 / 1
Heavy atoms 41
Fraction sp³ C 0.58
Formula C₂₆H₄₁BN₄O₁₀

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 212.6
  • −1 ≤ LogP ≤ 5 0.84
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 580.4
  • LogP ≤ 5 0.84
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 212.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
B([C@@H](C)NC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(=O)CC[C@@H](C(=O)O)NC(=O)OC(C)(C)C)(O)O
InChI 
InChI=1S/C26H41BN4O10/c1-17(27(38)39)29-22(33)19(12-8-9-15-28-24(36)40-16-18-10-6-5-7-11-18)30-21(32)14-13-20(23(34)35)31-25(37)41-26(2,3)4/h5-7,10-11,17,19-20,38-39H,8-9,12-16H2,1-4H3,(H,28,36)(H,29,33)(H,30,32)(H,31,37)(H,34,35)/t17-,19+,20+/m1/s1
InChIKey 
OTTYWVUOPWENAJ-HOJAQTOUSA-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
PF00768

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_1655.

PDB 13

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)