Ligand profile

465

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 3uxe UniProt P16083 Formula C₁₃H₁₀ClN₅O₂
Mol. weight 303.71 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
465
PDB
3uxe
UniProt (similar protein)
P16083
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 303.71 Da
LogP (Crippen) 1.49
H-bond donors 2
H-bond acceptors 5
TPSA 114.67 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 21
Fraction sp³ C 0.08
Formula C₁₃H₁₀ClN₅O₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 114.7
  • −1 ≤ LogP ≤ 5 1.49
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 303.7
  • LogP ≤ 5 1.49
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 114.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1c2c3c(cc(nc3c(c(c2N)Cl)N=C)C(=O)N)C1=O
InChI 
InChI=1S/C13H10ClN5O2/c1-17-10-7(14)8(15)11-6-4(13(21)19(11)2)3-5(12(16)20)18-9(6)10/h3H,1,15H2,2H3,(H2,16,20)
InChIKey 
IRLASAQBVTZKMT-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)