Ligand profile

BDR

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

Bound to: KP13_05551 — Periplasmic binding protein/LacI transcriptional regulator family protein

Via homolog PDB 3ksm UniProt Q2S7D2 Formula C₅H₁₀O₅
Mol. weight 150.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BDR
PDB
3ksm
UniProt (similar protein)
Q2S7D2
Target protein
KP13_05551

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 150.13 Da
LogP (Crippen) -2.58
H-bond donors 4
H-bond acceptors 5
TPSA 90.15 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 10
Fraction sp³ C 1.00
Formula C₅H₁₀O₅

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 90.2
  • −1 ≤ LogP ≤ 5 -2.58
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 150.1
  • LogP ≤ 5 -2.58
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 90.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]1[C@H]([C@H]([C@@H](O1)O)O)O)O
InChI 
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5-/m1/s1
InChIKey 
HMFHBZSHGGEWLO-TXICZTDVSA-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_05551.

PDB 2

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)