Ligand profile

5VD

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

Bound to: VK055_1078 — short chain dehydrogenase family protein

Via homolog PDB 5f5n UniProt A0A023GUL3 Formula C₂₁H₁₈O₉
Mol. weight 414.37 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
5VD
PDB
5f5n
UniProt (similar protein)
A0A023GUL3
Target protein
VK055_1078

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 414.37 Da
LogP (Crippen) 1.02
H-bond donors 5
H-bond acceptors 9
TPSA 161.59 Ų
Rotatable bonds 1
Aromatic rings 2 / 4
Heavy atoms 30
Fraction sp³ C 0.29
Formula C₂₁H₁₈O₉

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 161.6
  • −1 ≤ LogP ≤ 5 1.02
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 414.4
  • LogP ≤ 5 1.02
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 161.6
PAINS Alert

Matches PAINS filter: quinone_A(370). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@]1(C[C@@H](c2c(cc3c(c2O)C(=O)c4c(ccc(c4C3=O)O)O)[C@H]1C(=O)OC)O)O
InChI 
InChI=1S/C21H18O9/c1-21(29)6-11(24)12-7(16(21)20(28)30-2)5-8-13(18(12)26)19(27)15-10(23)4-3-9(22)14(15)17(8)25/h3-5,11,16,22-24,26,29H,6H2,1-2H3/t11-,16-,21+/m0/s1
InChIKey 
ZBSRQGXAWDQXFX-SBOBAANCSA-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
PF05368

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_1078.

PDB 3

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

Ligand PDB entry

ChEMBL 1

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

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)