Ligand profile

ZINC4513757

Virtual-screening candidate from ZINC.

Bound to: VK055_0098 — ribosomal RNA small subunit methyltransferase F

Via homolog UniProt Q60343 Formula C₁₀H₁₁N₅O₅
Tanimoto 0.65
Mol. weight 281.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4513757
UniProt (similar protein)
Q60343
Tanimoto
0.648
Target protein
VK055_0098

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 281.23 Da
LogP (Crippen) -1.89
H-bond donors 4
H-bond acceptors 9
TPSA 156.61 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.40
Formula C₁₀H₁₁N₅O₅

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 156.6
  • −1 ≤ LogP ≤ 5 -1.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 281.2
  • LogP ≤ 5 -1.89
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 156.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ncnc2c1ncn2[C@H]1O[C@@H](C(=O)O)[C@@H](O)[C@@H]1O
InChI 
InChI=1S/C10H11N5O5/c11-7-3-8(13-1-12-7)15(2-14-3)9-5(17)4(16)6(20-9)10(18)19/h1-2,4-6,9,16-17H,(H,18,19)(H2,11,12,13)/t4-,5-,6+,9-/m0/s1
InChIKey 
IBYWUFHJUDTSOC-CRBZEHORSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
SFG
Homolog
Q60343

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_0098.

PDB 1

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 4

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)