Ligand profile

ZINC5439936

Virtual-screening candidate from ZINC.

Bound to: VK055_4032 — flavodoxin-like fold family protein

Via homolog UniProt P16083 Formula C₂₅H₂₇NO₉
Tanimoto 0.74
Mol. weight 485.49 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5439936
UniProt (similar protein)
P16083
Tanimoto
0.743
Target protein
VK055_4032

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 485.49 Da
LogP (Crippen) 1.07
H-bond donors 5
H-bond acceptors 10
TPSA 168.77 Ų
Rotatable bonds 3
Aromatic rings 2 / 5
Heavy atoms 35
Fraction sp³ C 0.44
Formula C₂₅H₂₇NO₉

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 168.8
  • −1 ≤ LogP ≤ 5 1.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 485.5
  • LogP ≤ 5 1.07
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 168.8
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 
COc1cccc2c1C(=O)c1c(O)c3c(c(O)c1C2=O)C[C@@H](O)C[C@H]3O[C@H]1C[C@@H](N)[C@@H](O)[C@@H](C)O1
InChI 
InChI=1S/C25H27NO9/c1-9-21(28)13(26)8-16(34-9)35-15-7-10(27)6-12-18(15)25(32)20-19(23(12)30)22(29)11-4-3-5-14(33-2)17(11)24(20)31/h3-5,9-10,13,15-16,21,27-28,30,32H,6-8,26H2,1-2H3/t9-,10-,13-,15-,16+,21+/m1/s1
InChIKey 
PILBYTNNIUDJPF-HHZNLSNISA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
DM2
Homolog
P16083

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_4032.

PDB 38

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

Ligand PDB entry

ChEMBL 100

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

Compound Potency (pchembl)

ZINC 49

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

Compound Similarity (Tanimoto)