Ligand profile

6A1

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 3tem UniProt P16083 Formula C₁₉H₂₅N₄O₃⁺
Mol. weight 357.43 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6A1
PDB
3tem
UniProt (similar protein)
P16083
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 357.43 Da
LogP (Crippen) 2.24
H-bond donors 3
H-bond acceptors 6
TPSA 79.02 Ų
Rotatable bonds 5
Aromatic rings 3 / 4
Heavy atoms 26
Fraction sp³ C 0.42
Formula C₁₉H₂₅N₄O₃⁺

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 79.0
  • −1 ≤ LogP ≤ 5 2.24
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 357.4
  • LogP ≤ 5 2.24
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 79.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[N+](C)(CCNC1CCc2c3c1c(c4cc(ccc4n3cn2)OC)O)O
InChI 
InChI=1S/C19H24N4O3/c1-23(2,25)9-8-20-14-5-6-15-18-17(14)19(24)13-10-12(26-3)4-7-16(13)22(18)11-21-15/h4,7,10-11,14,20,25H,5-6,8-9H2,1-3H3/p+1
InChIKey 
VTPADFJSUDVABF-UHFFFAOYSA-O

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)