Binder profile

MB3

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

Bound to: PA4407 — cell division protein FtsZ

Via homolog PDB 6rvp UniProt P0A031 C5H9NO
Mol. weight 99.13 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MB3
PDB
6rvp
UniProt (similar protein)
P0A031
Target protein
PA4407

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 99.13 Da
LogP (Crippen) 0.24
H-bond donors 0
H-bond acceptors 1
TPSA 20.31 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 7
Fraction sp³ C 0.80
Formula C5H9NO

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 99.1
  • LogP ≤ 5 0.24
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 20.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CCCC1=O
InChI 
InChI=1S/C5H9NO/c1-6-4-2-3-5(6)7/h2-4H2,1H3
InChIKey 
SECXISVLQFMRJM-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00091

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA4407.

PDB 1

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

Ligand PDB entry

ChEMBL 27

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)