Ligand profile

936

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 1kbq UniProt P15559 Formula C₁₈H₁₆N₂O₆
Mol. weight 356.33 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
936
PDB
1kbq
UniProt (similar protein)
P15559
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 356.33 Da
LogP (Crippen) 2.73
H-bond donors 0
H-bond acceptors 7
TPSA 100.67 Ų
Rotatable bonds 5
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.22
Formula C₁₈H₁₆N₂O₆

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 100.7
  • −1 ≤ LogP ≤ 5 2.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 356.3
  • LogP ≤ 5 2.73
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 100.7
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 
Cc1c(c2c(n1C)C(=O)C=C(C2=O)OC)COc3ccc(cc3)[N+](=O)[O-]
InChI 
InChI=1S/C18H16N2O6/c1-10-13(9-26-12-6-4-11(5-7-12)20(23)24)16-17(19(10)2)14(21)8-15(25-3)18(16)22/h4-8H,9H2,1-3H3
InChIKey 
IBLWSLZYYZHSRG-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)