Ligand profile

RH1

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 1h66 UniProt P15559 Formula C₁₂H₁₄N₂O₃
Mol. weight 234.25 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
RH1
PDB
1h66
UniProt (similar protein)
P15559
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 234.25 Da
LogP (Crippen) -0.71
H-bond donors 1
H-bond acceptors 5
TPSA 60.39 Ų
Rotatable bonds 3
Aromatic rings 0 / 3
Heavy atoms 17
Fraction sp³ C 0.50
Formula C₁₂H₁₄N₂O₃

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 60.4
  • −1 ≤ LogP ≤ 5 -0.71
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 234.3
  • LogP ≤ 5 -0.71
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 60.4
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 
CC1=C(C(=O)C(=C(C1=O)N2CC2)CO)N3CC3
InChI 
InChI=1S/C12H14N2O3/c1-7-9(13-2-3-13)12(17)8(6-15)10(11(7)16)14-4-5-14/h15H,2-6H2,1H3
InChIKey 
JKDLOGLNPDVUCX-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)