Ligand profile

M49

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 4gqi UniProt P16083 Formula C₁₄H₁₇N₃O₃
Mol. weight 275.31 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
M49
PDB
4gqi
UniProt (similar protein)
P16083
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 275.31 Da
LogP (Crippen) 1.21
H-bond donors 3
H-bond acceptors 3
TPSA 87.30 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 20
Fraction sp³ C 0.36
Formula C₁₄H₁₇N₃O₃

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 87.3
  • −1 ≤ LogP ≤ 5 1.21
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 275.3
  • LogP ≤ 5 1.21
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 87.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)NCC[C@@H]1c2cc(ccc2NC1=O)NC(=O)C
InChI 
InChI=1S/C14H17N3O3/c1-8(18)15-6-5-11-12-7-10(16-9(2)19)3-4-13(12)17-14(11)20/h3-4,7,11H,5-6H2,1-2H3,(H,15,18)(H,16,19)(H,17,20)/t11-/m1/s1
InChIKey 
AFKNIIZCTCAFIO-LLVKDONJSA-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)