Ligand profile

ZINC257373216

Virtual-screening candidate from ZINC.

Bound to: VK055_4939 — cytidine deaminase

Via homolog UniProt P56389 Formula C₁₀H₁₅N₃O₅
Tanimoto 0.76
Mol. weight 257.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC257373216
UniProt (similar protein)
P56389
Tanimoto
0.756
Target protein
VK055_4939

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 257.25 Da
LogP (Crippen) -1.91
H-bond donors 3
H-bond acceptors 8
TPSA 119.83 Ų
Rotatable bonds 3
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.60
Formula C₁₀H₁₅N₃O₅

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 119.8
  • −1 ≤ LogP ≤ 5 -1.91
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 257.2
  • LogP ≤ 5 -1.91
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 119.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CO[C@@H]1[C@H](O)[C@H](CO)O[C@H]1n1ccc(N)nc1=O
InChI 
InChI=1S/C10H15N3O5/c1-17-8-7(15)5(4-14)18-9(8)13-3-2-6(11)12-10(13)16/h2-3,5,7-9,14-15H,4H2,1H3,(H2,11,12,16)/t5-,7+,8+,9+/m0/s1
InChIKey 
RFCQJGFZUQFYRF-KDBVAPGDSA-N

Provenance

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

Method
LigQ nearest_k
Query
CTN
Homolog
P56389

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)