Ligand profile

DCZ

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

Bound to: VK055_0016 — cytosine-specific methyltransferase

Via homolog PDB 2z6q UniProt P05102 Formula C₉H₁₃N₃O₄
Mol. weight 227.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DCZ
PDB
2z6q
UniProt (similar protein)
P05102
Target protein
VK055_0016

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 227.22 Da
LogP (Crippen) -1.53
H-bond donors 3
H-bond acceptors 7
TPSA 110.60 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 16
Fraction sp³ C 0.56
Formula C₉H₁₃N₃O₄

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 110.6
  • −1 ≤ LogP ≤ 5 -1.53
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 227.2
  • LogP ≤ 5 -1.53
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 110.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO)O
InChI 
InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m0/s1
InChIKey 
CKTSBUTUHBMZGZ-SHYZEUOFSA-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
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 2

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 50

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

Compound Similarity (Tanimoto)