Ligand profile

CTD

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

Bound to: VK055_4939 — cytidine deaminase

Via homolog PDB 1aln UniProt P0ABF6 Formula C₁₀H₁₄N₂O₅
Mol. weight 242.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CTD
PDB
1aln
UniProt (similar protein)
P0ABF6
Target protein
VK055_4939

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 242.23 Da
LogP (Crippen) -1.96
H-bond donors 4
H-bond acceptors 7
TPSA 117.94 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 17
Fraction sp³ C 0.50
Formula C₁₀H₁₄N₂O₅

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 117.9
  • −1 ≤ LogP ≤ 5 -1.96
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 242.2
  • LogP ≤ 5 -1.96
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 117.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CN(C(=O)C=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
InChI 
InChI=1S/C10H14N2O5/c11-5-1-2-12(7(14)3-5)10-9(16)8(15)6(4-13)17-10/h1-3,6,8-10,13,15-16H,4,11H2/t6-,8-,9-,10-/m1/s1
InChIKey 
OGADSZTVCUXSOK-PEBGCTIMSA-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' 'PF08211

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 8

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 50

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

Compound Similarity (Tanimoto)