Ligand profile

M9F

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

Bound to: VK055_4546 — 2OG-Fe(II) oxygenase superfamily protein

Via homolog PDB 2y6f UniProt P05326 Formula C₁₄H₂₅N₃O₆S₂
Mol. weight 395.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
M9F
PDB
2y6f
UniProt (similar protein)
P05326
Target protein
VK055_4546

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 395.50 Da
LogP (Crippen) -0.70
H-bond donors 6
H-bond acceptors 7
TPSA 158.82 Ų
Rotatable bonds 12
Aromatic rings 0 / 0
Heavy atoms 25
Fraction sp³ C 0.71
Formula C₁₄H₂₅N₃O₆S₂

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 158.8
  • −1 ≤ LogP ≤ 5 -0.70
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 395.5
  • LogP ≤ 5 -0.70
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 158.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC([C@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C@@H](C(=O)O)N)SC
InChI 
InChI=1S/C14H25N3O6S2/c1-7(25-2)11(14(22)23)17-12(19)9(6-24)16-10(18)5-3-4-8(15)13(20)21/h7-9,11,24H,3-6,15H2,1-2H3,(H,16,18)(H,17,19)(H,20,21)(H,22,23)/t7?,8-,9-,11+/m0/s1
InChIKey 
STWWPNPLTMLLPP-MHSYOIBSSA-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
PF03171' 'PF14226

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_4546.

PDB 31

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)