Ligand profile

MTH

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

Bound to: VK055_2391 — MTA/SAH nucleosidase

Via homolog PDB 1nc1 UniProt P0AF12 Formula C₁₂H₁₆N₄O₃S
Mol. weight 296.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MTH
PDB
1nc1
UniProt (similar protein)
P0AF12
Target protein
VK055_2391

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 296.35 Da
LogP (Crippen) -0.00
H-bond donors 3
H-bond acceptors 8
TPSA 106.42 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.50
Formula C₁₂H₁₆N₄O₃S

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 106.4
  • −1 ≤ LogP ≤ 5 -0.00
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 296.4
  • LogP ≤ 5 -0.00
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 106.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2ccc3c2ncnc3N)O)O
InChI 
InChI=1S/C12H16N4O3S/c1-20-4-7-8(17)9(18)12(19-7)16-3-2-6-10(13)14-5-15-11(6)16/h2-3,5,7-9,12,17-18H,4H2,1H3,(H2,13,14,15)/t7-,8-,9-,12-/m1/s1
InChIKey 
WBPLMFVTQMIPLW-MFYTUXHUSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF01048

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_2391.

PDB 10

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

Ligand PDB entry

ChEMBL 34

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)