Ligand profile

ECA

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

Bound to: VK055_0361 — putative ferrichrome-binding protein

Via homolog PDB 2xv1 UniProt P40409 Formula C₃₀H₂₇N₃O₉
Mol. weight 573.56 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ECA
PDB
2xv1
UniProt (similar protein)
P40409
Target protein
VK055_0361

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 573.56 Da
LogP (Crippen) 2.71
H-bond donors 9
H-bond acceptors 9
TPSA 208.68 Ų
Rotatable bonds 9
Aromatic rings 4 / 4
Heavy atoms 42
Fraction sp³ C 0.10
Formula C₃₀H₂₇N₃O₉

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 208.7
  • −1 ≤ LogP ≤ 5 2.71
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 573.6
  • LogP ≤ 5 2.71
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 208.7
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c(c(c1)O)O)C(=O)NCc2cc(cc(c2)CNC(=O)c3cccc(c3O)O)CNC(=O)c4cccc(c4O)O
InChI 
InChI=1S/C30H27N3O9/c34-22-7-1-4-19(25(22)37)28(40)31-13-16-10-17(14-32-29(41)20-5-2-8-23(35)26(20)38)12-18(11-16)15-33-30(42)21-6-3-9-24(36)27(21)39/h1-12,34-39H,13-15H2,(H,31,40)(H,32,41)(H,33,42)
InChIKey 
GCTFIRZGPIUOAK-UHFFFAOYSA-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
PF01497

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_0361.

PDB 3

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)