Ligand profile

MCF

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

Bound to: VK055_0432 — amidohydrolase family protein

Via homolog PDB 4gbd UniProt Q9HZ64 Formula C₁₂H₁₈N₄O₄S
Mol. weight 314.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MCF
PDB
4gbd
UniProt (similar protein)
Q9HZ64
Target protein
VK055_0432

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 314.37 Da
LogP (Crippen) -0.84
H-bond donors 4
H-bond acceptors 9
TPSA 112.13 Ų
Rotatable bonds 3
Aromatic rings 1 / 3
Heavy atoms 21
Fraction sp³ C 0.67
Formula C₁₂H₁₈N₄O₄S

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 112.1
  • −1 ≤ LogP ≤ 5 -0.84
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 314.4
  • LogP ≤ 5 -0.84
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 112.1
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)n2cnc3c2N=CNC[C@H]3O)O)O
InChI 
InChI=1S/C12H18N4O4S/c1-21-3-7-9(18)10(19)12(20-7)16-5-15-8-6(17)2-13-4-14-11(8)16/h4-7,9-10,12,17-19H,2-3H2,1H3,(H,13,14)/t6-,7-,9-,10-,12-/m1/s1
InChIKey 
QLPPCUVJNCMYFD-SANHVUMCSA-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
PF01979

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_0432.

PDB 6

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)