Ligand profile

SBH

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

Bound to: VK055_4165 — isopentenyl-diphosphate delta-isomerase

Via homolog PDB 1x83 UniProt Q46822 Formula C₅H₁₃BrO₈P₂
Mol. weight 343.00 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SBH
PDB
1x83
UniProt (similar protein)
Q46822
Target protein
VK055_4165

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 343.00 Da
LogP (Crippen) 0.75
H-bond donors 4
H-bond acceptors 5
TPSA 133.52 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 1.00
Formula C₅H₁₃BrO₈P₂

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 133.5
  • −1 ≤ LogP ≤ 5 0.75
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 343.0
  • LogP ≤ 5 0.75
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 133.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@](CCO[P@@](=O)(O)OP(=O)(O)O)(CBr)O
InChI 
InChI=1S/C5H13BrO8P2/c1-5(7,4-6)2-3-13-16(11,12)14-15(8,9)10/h7H,2-4H2,1H3,(H,11,12)(H2,8,9,10)/t5-/m0/s1
InChIKey 
YKAYCWPQDPILSA-YFKPBYRVSA-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
PF00293

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4165.

PDB 7

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

Ligand PDB entry

ChEMBL 2

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 7

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

Compound Similarity (Tanimoto)