Ligand profile

3VB

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

Bound to: KP13_01769 — putative ribose ABC transporter substrate-binding protein

Via homolog PDB 4rsm UniProt A0QYB5 Formula 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
KP13_01769

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.

  • TPSA ≤ 90 Ų 80.9
  • −1 ≤ LogP ≤ 5 -2.31
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 Target 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 ligands for this protein

Quick navigation to other ligands bound to KP13_01769.

PDB 3

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)