Ligand profile

SOD

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

Bound to: VK055_3293 — GTP-binding protein TypA/BipA

Via homolog PDB 2e1r UniProt P32324 Formula C₂₉H₃₉ClO₆
Mol. weight 519.08 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SOD
PDB
2e1r
UniProt (similar protein)
P32324
Target protein
VK055_3293

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 519.08 Da
LogP (Crippen) 4.85
H-bond donors 1
H-bond acceptors 5
TPSA 82.06 Ų
Rotatable bonds 6
Aromatic rings 0 / 6
Heavy atoms 36
Fraction sp³ C 0.79
Formula C₂₉H₃₉ClO₆

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 82.1
  • −1 ≤ LogP ≤ 5 4.85
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 519.1
  • LogP ≤ 5 4.85
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 82.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1[C@@H](C[C@@H]2[C@@H]1C[C@@]3([C@@H]4C[C@]2([C@]3(C(=C4)C(C)C)C(=O)O)C=O)CO[C@H]5C[C@@H]6[C@@H]([C@H](O5)C)OCC6=C)Cl
InChI 
InChI=1S/C29H39ClO6/c1-14(2)21-6-18-9-27(12-31)22-8-23(30)16(4)20(22)10-28(18,29(21,27)26(32)33)13-35-24-7-19-15(3)11-34-25(19)17(5)36-24/h6,12,14,16-20,22-25H,3,7-11,13H2,1-2,4-5H3,(H,32,33)/t16-,17+,18-,19-,20+,22+,23+,24+,25+,27-,28-,29-/m0/s1
InChIKey 
OFLZRRPTCKISFB-SHWNUAPTSA-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
PF00679' 'PF14492

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_3293.

PDB 7

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)