Ligand profile

CZ9

Ligand co-crystallized with this exact protein (Protein Data Bank).

Bound to: VK055_0891 — beta-lactamase SHV-24

Direct evidence PDB 3mxs UniProt P0AD64 Formula C₁₇H₂₃BN₄O₇
Mol. weight 406.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CZ9
PDB
3mxs
UniProt (this protein)
P0AD64
Target protein
VK055_0891

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 406.20 Da
LogP (Crippen) -2.17
H-bond donors 5
H-bond acceptors 7
TPSA 159.51 Ų
Rotatable bonds 7
Aromatic rings 1 / 2
Heavy atoms 29
Fraction sp³ C 0.41
Formula C₁₇H₂₃BN₄O₇

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 159.5
  • −1 ≤ LogP ≤ 5 -2.17
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 406.2
  • LogP ≤ 5 -2.17
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 159.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
B(CNC(=O)[C@@H](Cc1ccc(cc1)O)NC(=O)N2CCN(C(=O)C2=O)CC)(O)O
InChI 
InChI=1S/C17H23BN4O7/c1-2-21-7-8-22(16(26)15(21)25)17(27)20-13(14(24)19-10-18(28)29)9-11-3-5-12(23)6-4-11/h3-6,13,23,28-29H,2,7-10H2,1H3,(H,19,24)(H,20,27)/t13-/m1/s1
InChIKey 
INXKLMQPFNYGIK-CYBMUJFWSA-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
PF00144' 'PF13354

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_0891.

PDB 43

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

Ligand PDB entry

ChEMBL 100

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)