Ligand profile

CHEMBL5187655

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0016 — cytosine-specific methyltransferase

Via homolog UniProt P26358 Formula C₂₀H₂₇N₉O₇
pchembl 6.40 ~398.1 nM
Mol. weight 505.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5187655
UniProt (similar protein)
P26358
pchembl
6.400 (~398.1 nM)
Target protein
VK055_0016

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 505.49 Da
LogP (Crippen) -3.40
H-bond donors 7
H-bond acceptors 16
TPSA 241.94 Ų
Rotatable bonds 7
Aromatic rings 3 / 5
Heavy atoms 36
Fraction sp³ C 0.55
Formula C₂₀H₂₇N₉O₇

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 241.9
  • −1 ≤ LogP ≤ 5 -3.40
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 505.5
  • LogP ≤ 5 -3.40
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 241.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc(=O)n([C@H]2C[C@H](O)[C@@H](CO)O2)cc1CNC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O
InChI 
InChI=1S/C20H27N9O7/c21-16-8(4-28(20(34)27-16)12-1-9(31)11(5-30)35-12)2-23-3-10-14(32)15(33)19(36-10)29-7-26-13-17(22)24-6-25-18(13)29/h4,6-7,9-12,14-15,19,23,30-33H,1-3,5H2,(H2,21,27,34)(H2,22,24,25)/t9-,10+,11+,12+,14+,15+,19+/m0/s1
InChIKey 
WLNFAZVETQRDTE-SLFMBYJQSA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00145

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 13

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)