Ligand profile

CYT

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

Bound to: VK055_4780 — cytidine and deoxycytidylate deaminase zinc-binding region family protein

Via homolog PDB 4ld4 UniProt Q82Y41 Formula C₄H₅N₃O
Mol. weight 111.10 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CYT
PDB
4ld4
UniProt (similar protein)
Q82Y41
Target protein
VK055_4780

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 111.10 Da
LogP (Crippen) -0.65
H-bond donors 2
H-bond acceptors 3
TPSA 71.77 Ų
Rotatable bonds 0
Aromatic rings 1 / 1
Heavy atoms 8
Fraction sp³ C 0.00
Formula C₄H₅N₃O

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 71.8
  • −1 ≤ LogP ≤ 5 -0.65
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 111.1
  • LogP ≤ 5 -0.65
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 71.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=C(NC(=O)N=C1)N
InChI 
InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
InChIKey 
OPTASPLRGRRNAP-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
PF00383

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_4780.

PDB 11

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)