Ligand profile

BIG

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

Bound to: VK055_2391 — MTA/SAH nucleosidase

Via homolog PDB 4wkc UniProt A7ZHQ1 Formula C₁₆H₂₅N₅OS
Mol. weight 335.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BIG
PDB
4wkc
UniProt (similar protein)
A7ZHQ1
Target protein
VK055_2391

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 335.48 Da
LogP (Crippen) 1.87
H-bond donors 3
H-bond acceptors 6
TPSA 91.06 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.62
Formula C₁₆H₂₅N₅OS

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 91.1
  • −1 ≤ LogP ≤ 5 1.87
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 335.5
  • LogP ≤ 5 1.87
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 91.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCSC[C@H]1C[N@](C[C@@H]1O)Cc2c[nH]c3c2ncnc3N
InChI 
InChI=1S/C16H25N5OS/c1-2-3-4-23-9-12-7-21(8-13(12)22)6-11-5-18-15-14(11)19-10-20-16(15)17/h5,10,12-13,18,22H,2-4,6-9H2,1H3,(H2,17,19,20)/t12-,13+/m1/s1
InChIKey 
LTSUEVPGSXUJHT-OLZOCXBDSA-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)