Ligand profile

ZINC12503924

Virtual-screening candidate from ZINC.

Bound to: VK055_0016 — cytosine-specific methyltransferase

Via homolog UniProt P05102 Formula C₉H₁₄N₃O₇P
Tanimoto 0.72
Mol. weight 307.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12503924
UniProt (similar protein)
P05102
Tanimoto
0.723
Target protein
VK055_0016

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 307.20 Da
LogP (Crippen) -1.42
H-bond donors 4
H-bond acceptors 8
TPSA 157.13 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 20
Fraction sp³ C 0.56
Formula C₉H₁₄N₃O₇P

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 157.1
  • −1 ≤ LogP ≤ 5 -1.42
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 307.2
  • LogP ≤ 5 -1.42
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 157.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ccn([C@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)c(=O)n1
InChI 
InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6-,8-/m1/s1
InChIKey 
NCMVOABPESMRCP-ATRFCDNQSA-N

Provenance

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

Method
LigQ nearest_k
Query
DCZ
Homolog
P05102

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_0016.

PDB 3

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

Ligand PDB entry

ChEMBL 14

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)