Ligand profile

XM5

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

Bound to: VK055_2684 — ribosyldihydronicotinamide dehydrogenase (quinone)

Via homolog PDB 3g5m UniProt P16083 Formula C₁₂H₁₁NO₄
Mol. weight 233.22 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XM5
PDB
3g5m
UniProt (similar protein)
P16083
Target protein
VK055_2684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 233.22 Da
LogP (Crippen) 1.28
H-bond donors 0
H-bond acceptors 5
TPSA 49.69 Ų
Rotatable bonds 1
Aromatic rings 2 / 3
Heavy atoms 17
Fraction sp³ C 0.25
Formula C₁₂H₁₁NO₄

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 49.7
  • −1 ≤ LogP ≤ 5 1.28
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 233.2
  • LogP ≤ 5 1.28
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 49.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1c2c(ccc3c2OCO3)C(=CC1=O)OC
InChI 
InChI=1S/C12H11NO4/c1-13-10(14)5-9(15-2)7-3-4-8-12(11(7)13)17-6-16-8/h3-5H,6H2,1-2H3
InChIKey 
DPXXJCMMMXZVSW-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)