Binder profile

3VB

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

Bound to: PA1946 — ribose ABC transporter substrate-binding protein

Via homolog PDB 4rsm UniProt A0QYB5 C4H10O4
Mol. weight 122.12 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3VB
PDB
4rsm
UniProt (similar protein)
A0QYB5
Target protein
PA1946

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 122.12 Da
LogP (Crippen) -2.31
H-bond donors 4
H-bond acceptors 4
TPSA 80.92 Ų
Rotatable bonds 3
Aromatic rings 0 / 0
Heavy atoms 8
Fraction sp³ C 1.00
Formula C4H10O4

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 122.1
  • LogP ≤ 5 -2.31
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 80.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]([C@@H](CO)O)O)O
InChI 
InChI=1S/C4H10O4/c5-1-3(7)4(8)2-6/h3-8H,1-2H2/t3-,4-/m1/s1
InChIKey 
UNXHWFMMPAWVPI-QWWZWVQMSA-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
PF13407

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA1946.

PDB 1

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

Ligand PDB entry

ZINC 25

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)