Ligand profile

MTM

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

Bound to: VK055_2391 — MTA/SAH nucleosidase

Via homolog PDB 1y6r UniProt P0AF12 Formula C₁₂H₁₉N₅O₂S
Mol. weight 297.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MTM
PDB
1y6r
UniProt (similar protein)
P0AF12
Target protein
VK055_2391

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 297.38 Da
LogP (Crippen) -0.67
H-bond donors 6
H-bond acceptors 7
TPSA 118.69 Ų
Rotatable bonds 3
Aromatic rings 1 / 3
Heavy atoms 20
Fraction sp³ C 0.58
Formula C₁₂H₁₉N₅O₂S

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 118.7
  • −1 ≤ LogP ≤ 5 -0.67
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 297.4
  • LogP ≤ 5 -0.67
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 118.7
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](N1)c2c[nH]c3c2N=CNC3N)O)O
InChI 
InChI=1S/C12H19N5O2S/c1-20-3-6-10(18)11(19)8(17-6)5-2-14-9-7(5)15-4-16-12(9)13/h2,4,6,8,10-12,14,17-19H,3,13H2,1H3,(H,15,16)/t6-,8+,10-,11+,12?/m1/s1
InChIKey 
YLCQGEBEQIBOOJ-BOFBLULFSA-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)