Ligand profile

NPB

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

Bound to: KP13_06703 — Carbepenem-hydrolyzing beta-lactamase KPC2

Direct evidence PDB 3rxx UniProt Q9F663 Formula C₆H₆BNO₄
Mol. weight 166.93 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NPB
PDB
3rxx
UniProt (this protein)
Q9F663
Target protein
KP13_06703

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 166.93 Da
LogP (Crippen) -0.73
H-bond donors 2
H-bond acceptors 4
TPSA 83.60 Ų
Rotatable bonds 2
Aromatic rings 1 / 1
Heavy atoms 12
Fraction sp³ C 0.00
Formula C₆H₆BNO₄

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 83.6
  • −1 ≤ LogP ≤ 5 -0.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 166.9
  • LogP ≤ 5 -0.73
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 83.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
B(c1cccc(c1)[N+](=O)[O-])(O)O
InChI 
InChI=1S/C6H6BNO4/c9-7(10)5-2-1-3-6(4-5)8(11)12/h1-4,9-10H
InChIKey 
ZNRGSYUVFVNSAW-UHFFFAOYSA-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 KP13_06703.

PDB 35

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)