Ligand profile

HB0

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

Bound to: KP13_03889 — putative diguanylate phosphodiesterase

Via homolog PDB 4lj3 UniProt P21514 Formula C₇H₁₄O₂
Mol. weight 130.19 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HB0
PDB
4lj3
UniProt (similar protein)
P21514
Target protein
KP13_03889

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 130.19 Da
LogP (Crippen) 0.53
H-bond donors 2
H-bond acceptors 2
TPSA 40.46 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 9
Fraction sp³ C 1.00
Formula C₇H₁₄O₂

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.

  • TPSA ≤ 90 Ų 40.5
  • −1 ≤ LogP ≤ 5 0.53
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 130.2
  • LogP ≤ 5 0.53
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 40.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CC(CCC1CO)O
InChI 
InChI=1S/C7H14O2/c8-5-6-1-3-7(9)4-2-6/h6-9H,1-5H2
InChIKey 
VGRZISGVNOKTQU-UHFFFAOYSA-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
PF00563

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_03889.

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)