Ligand profile

SO1

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

Bound to: VK055_3750 — translation elongation factor Tu

Via homolog PDB 2p8z UniProt P60339 Formula C₂₇H₄₂O₈
Mol. weight 494.63 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SO1
PDB
2p8z
UniProt (similar protein)
P60339
Target protein
VK055_3750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 494.63 Da
LogP (Crippen) 2.49
H-bond donors 3
H-bond acceptors 7
TPSA 122.52 Ų
Rotatable bonds 7
Aromatic rings 0 / 5
Heavy atoms 35
Fraction sp³ C 0.93
Formula C₂₇H₄₂O₈

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 122.5
  • −1 ≤ LogP ≤ 5 2.49
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 494.6
  • LogP ≤ 5 2.49
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 122.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1CC[C@@H]2[C@@H]1C[C@@]3([C@H]4CC([C@@]3([C@@]2(C4)C=O)C(=O)O)C(C)C)CO[C@H]5[C@H]([C@@H]([C@@H]([C@H](O5)C)OC)O)O
InChI 
InChI=1S/C27H42O8/c1-13(2)19-8-16-9-25(11-28)18-7-6-14(3)17(18)10-26(16,27(19,25)24(31)32)12-34-23-21(30)20(29)22(33-5)15(4)35-23/h11,13-23,29-30H,6-10,12H2,1-5H3,(H,31,32)/t14-,15-,16+,17-,18-,19?,20+,21+,22-,23-,25+,26+,27+/m1/s1
InChIKey 
DIBGPTPYRVEPSP-OHFCZZTFSA-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_3750.

PDB 19

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)