Ligand profile

F9E

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

Bound to: VK055_2050 — yjdL peptide transporter

Via homolog PDB 6gs4 UniProt P77304 Formula C₁₄H₂₂N₆O₅
Mol. weight 354.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
F9E
PDB
6gs4
UniProt (similar protein)
P77304
Target protein
VK055_2050

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 354.37 Da
LogP (Crippen) -1.44
H-bond donors 4
H-bond acceptors 10
TPSA 171.37 Ų
Rotatable bonds 8
Aromatic rings 2 / 2
Heavy atoms 25
Fraction sp³ C 0.57
Formula C₁₄H₂₂N₆O₅

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 171.4
  • −1 ≤ LogP ≤ 5 -1.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 354.4
  • LogP ≤ 5 -1.44
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 171.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@@H](C(=O)OC[C@H](CO)OCn1cnc2c1NC(=NC2=O)N)N
InChI 
InChI=1S/C14H22N6O5/c1-7(2)9(15)13(23)24-4-8(3-21)25-6-20-5-17-10-11(20)18-14(16)19-12(10)22/h5,7-9,21H,3-4,6,15H2,1-2H3,(H3,16,18,19,22)/t8-,9-/m0/s1
InChIKey 
WPVFJKSGQUFQAP-IUCAKERBSA-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
PF00854

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_2050.

PDB 13

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)