Ligand profile

E09

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 1gg5 UniProt P15559 Formula C₁₅H₁₈N₂O₄
Mol. weight 290.32 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
E09
PDB
1gg5
UniProt (similar protein)
P15559
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 290.32 Da
LogP (Crippen) 0.02
H-bond donors 2
H-bond acceptors 6
TPSA 82.54 Ų
Rotatable bonds 5
Aromatic rings 1 / 3
Heavy atoms 21
Fraction sp³ C 0.47
Formula C₁₅H₁₈N₂O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 82.5
  • −1 ≤ LogP ≤ 5 0.02
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 290.3
  • LogP ≤ 5 0.02
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 82.5
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 
Cn1c(c(c2c1C(=O)C=C(C2=O)N3CC3)CO)CCCO
InChI 
InChI=1S/C15H18N2O4/c1-16-10(3-2-6-18)9(8-19)13-14(16)12(20)7-11(15(13)21)17-4-5-17/h7,18-19H,2-6,8H2,1H3
InChIKey 
JCCDRCRHGKFTQS-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
PF02525

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_2684.

PDB 59

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 50

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

Compound Similarity (Tanimoto)