Ligand profile

THU

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

Bound to: VK055_4939 — cytidine deaminase

Via homolog PDB 1jtk UniProt P19079 Formula C₉H₁₄N₂O₅
Mol. weight 230.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
THU
PDB
1jtk
UniProt (similar protein)
P19079
Target protein
VK055_4939

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 230.22 Da
LogP (Crippen) -1.60
H-bond donors 3
H-bond acceptors 5
TPSA 99.10 Ų
Rotatable bonds 2
Aromatic rings 0 / 2
Heavy atoms 16
Fraction sp³ C 0.78
Formula C₉H₁₄N₂O₅

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 99.1
  • −1 ≤ LogP ≤ 5 -1.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 230.2
  • LogP ≤ 5 -1.60
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 99.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CN(C(=O)NC1=O)C2C[C@@H]([C@H](O2)CO)O
InChI 
InChI=1S/C9H14N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h5-6,8,12-13H,1-4H2,(H,10,14,15)/t5-,6+,8?/m0/s1
InChIKey 
XMJRLEURHMTTRX-FWHJPCMOSA-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_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)