Ligand profile

NBF

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

Bound to: KP13_03128 — Beta-lactamase CTX-M-2

Via homolog PDB 1yms UniProt Q9L5C8 Formula C₁₄H₁₆BNO₄
Mol. weight 273.10 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NBF
PDB
1yms
UniProt (similar protein)
Q9L5C8
Target protein
KP13_03128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 273.10 Da
LogP (Crippen) 0.98
H-bond donors 3
H-bond acceptors 4
TPSA 78.79 Ų
Rotatable bonds 5
Aromatic rings 2 / 2
Heavy atoms 20
Fraction sp³ C 0.21
Formula C₁₄H₁₆BNO₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 78.8
  • −1 ≤ LogP ≤ 5 0.98
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 273.1
  • LogP ≤ 5 0.98
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 78.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
B(CNC(=O)c1c2ccccc2ccc1OCC)(O)O
InChI 
InChI=1S/C14H16BNO4/c1-2-20-12-8-7-10-5-3-4-6-11(10)13(12)14(17)16-9-15(18)19/h3-8,18-19H,2,9H2,1H3,(H,16,17)
InChIKey 
VGXJNGVFESCMME-UHFFFAOYSA-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
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 KP13_03128.

PDB 51

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

Ligand PDB entry

ChEMBL 6

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)