Ligand profile

AD1

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 2qmy UniProt P16083 Formula C₉H₉NO₃
Mol. weight 179.17 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
AD1
PDB
2qmy
UniProt (similar protein)
P16083
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 179.17 Da
LogP (Crippen) -0.75
H-bond donors 1
H-bond acceptors 4
TPSA 57.61 Ų
Rotatable bonds 0
Aromatic rings 0 / 2
Heavy atoms 13
Fraction sp³ C 0.33
Formula C₉H₉NO₃

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 57.6
  • −1 ≤ LogP ≤ 5 -0.75
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 179.2
  • LogP ≤ 5 -0.75
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 57.6
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 
CN1C[C@H](C2=CC(=O)C(=O)C=C21)O
InChI 
InChI=1S/C9H9NO3/c1-10-4-9(13)5-2-7(11)8(12)3-6(5)10/h2-3,9,13H,4H2,1H3/t9-/m1/s1
InChIKey 
RPHLQSHHTJORHI-SECBINFHSA-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)