Binder profile

VKC

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

Bound to: PA2745 — hydrolase

Via homolog PDB 4ccw UniProt Q59248 C4H8O4
Mol. weight 120.10 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VKC
PDB
4ccw
UniProt (similar protein)
Q59248
Target protein
PA2745

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 120.10 Da
LogP (Crippen) -0.92
H-bond donors 2
H-bond acceptors 3
TPSA 66.76 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 8
Fraction sp³ C 0.75
Formula C4H8O4

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 120.1
  • LogP ≤ 5 -0.92
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 66.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(COCC(=O)O)O
InChI 
InChI=1S/C4H8O4/c5-1-2-8-3-4(6)7/h5H,1-3H2,(H,6,7)
InChIKey 
VDNMIIDPBBCMTM-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
PF00561

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA2745.

PDB 5

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

Ligand PDB entry

ChEMBL 4

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)