Ligand profile

E9C

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

Bound to: VK055_1043 — primary amine oxidase

Via homolog PDB 6l9c UniProt P46881 Formula C₉H₉NO₅
Mol. weight 211.17 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
E9C
PDB
6l9c
UniProt (similar protein)
P46881
Target protein
VK055_1043

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 211.17 Da
LogP (Crippen) -1.17
H-bond donors 2
H-bond acceptors 5
TPSA 114.53 Ų
Rotatable bonds 3
Aromatic rings 0 / 1
Heavy atoms 15
Fraction sp³ C 0.33
Formula C₉H₉NO₅

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 114.5
  • −1 ≤ LogP ≤ 5 -1.17
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 211.2
  • LogP ≤ 5 -1.17
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 114.5
PAINS Alert

Matches PAINS filter: imine_one_A(321). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1C(=O)C(=CC(=O)C1=O)C[C@@H](C(=O)O)N
InChI 
InChI=1S/C9H9NO5/c10-5(9(14)15)1-4-2-7(12)8(13)3-6(4)11/h2,5H,1,3,10H2,(H,14,15)/t5-/m0/s1
InChIKey 
YEQCWDUWMMTDJJ-YFKPBYRVSA-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
PF01179

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_1043.

PDB 14

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

Ligand PDB entry

ChEMBL 9

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)