Ligand profile

ZINC34248202

Virtual-screening candidate from ZINC.

Bound to: VK055_4939 — cytidine deaminase

Via homolog UniProt Q9KSM5 Formula C₉H₁₃N₃O₅
Tanimoto 0.80
Mol. weight 243.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC34248202
UniProt (similar protein)
Q9KSM5
Tanimoto
0.800
Target protein
VK055_4939

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 243.22 Da
LogP (Crippen) -2.89
H-bond donors 4
H-bond acceptors 7
TPSA 130.57 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 17
Fraction sp³ C 0.56
Formula C₉H₁₃N₃O₅

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 130.6
  • −1 ≤ LogP ≤ 5 -2.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 243.2
  • LogP ≤ 5 -2.89
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 130.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@H]1[C@H](O)[C@@H](CO)O[C@H]1n1ccc(=O)[nH]c1=O
InChI 
InChI=1S/C9H13N3O5/c10-6-7(15)4(3-13)17-8(6)12-2-1-5(14)11-9(12)16/h1-2,4,6-8,13,15H,3,10H2,(H,11,14,16)/t4-,6+,7-,8-/m1/s1
InChIKey 
LLIPTMWIZVIUSX-PXBUCIJWSA-N

Provenance

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

Method
LigQ nearest_k
Query
URI
Homolog
Q9KSM5

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_4939.

PDB 9

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

Ligand PDB entry

ChEMBL 16

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)