Ligand profile

7XF

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

Bound to: VK055_2825 — cys/Met metabolism PLP-dependent enzyme family protein

Via homolog PDB 5x30 UniProt P13254 Formula C₁₂H₁₉N₂O₇PS
Mol. weight 366.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7XF
PDB
5x30
UniProt (similar protein)
P13254
Target protein
VK055_2825

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 366.33 Da
LogP (Crippen) 0.57
H-bond donors 6
H-bond acceptors 7
TPSA 149.21 Ų
Rotatable bonds 9
Aromatic rings 1 / 1
Heavy atoms 23
Fraction sp³ C 0.50
Formula C₁₂H₁₉N₂O₇PS

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 149.2
  • −1 ≤ LogP ≤ 5 0.57
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 366.3
  • LogP ≤ 5 0.57
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 149.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCS)C(=O)O)O
InChI 
InChI=1S/C12H19N2O7PS/c1-7-11(15)9(5-14-10(2-3-23)12(16)17)8(4-13-7)6-21-22(18,19)20/h4,10,14-15,23H,2-3,5-6H2,1H3,(H,16,17)(H2,18,19,20)/t10-/m0/s1
InChIKey 
PXCMMZUTCUCUSM-JTQLQIEISA-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
PF01053

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_2825.

PDB 5

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)