Ligand profile

340

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 1kbo UniProt P15559 Formula C₁₈H₁₇NO₄
Mol. weight 311.34 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
340
PDB
1kbo
UniProt (similar protein)
P15559
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 311.34 Da
LogP (Crippen) 2.82
H-bond donors 0
H-bond acceptors 5
TPSA 57.53 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.22
Formula C₁₈H₁₇NO₄

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 57.5
  • −1 ≤ LogP ≤ 5 2.82
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 311.3
  • LogP ≤ 5 2.82
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 57.5
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 
Cc1c(c2c(n1C)C(=O)C=C(C2=O)OC)COc3ccccc3
InChI 
InChI=1S/C18H17NO4/c1-11-13(10-23-12-7-5-4-6-8-12)16-17(19(11)2)14(20)9-15(22-3)18(16)21/h4-9H,10H2,1-3H3
InChIKey 
JRPJCFILHCLEJI-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)