Ligand profile

THM

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

Bound to: VK055_2857 — 2',3'-cyclic-nucleotide 2'-phosphodiesterase

Via homolog PDB 2z1a UniProt Q5SIP1 Formula C₁₀H₁₄N₂O₅
Mol. weight 242.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
THM
PDB
2z1a
UniProt (similar protein)
Q5SIP1
Target protein
VK055_2857

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 242.23 Da
LogP (Crippen) -1.51
H-bond donors 3
H-bond acceptors 6
TPSA 104.55 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 17
Fraction sp³ C 0.60
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 104.6
  • −1 ≤ LogP ≤ 5 -1.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 242.2
  • LogP ≤ 5 -1.51
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 104.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O
InChI 
InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1
InChIKey 
IQFYYKKMVGJFEH-XLPZGREQSA-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
PF00149' 'PF02872

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_2857.

PDB 8

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)