Ligand profile

LPP

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

Bound to: VK055_2353 — D-methionine ABC transporter, ATP-binding protein

Via homolog PDB 7cha UniProt Q9HVW1 Formula C₃₅H₆₉O₈P
Mol. weight 648.90 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LPP
PDB
7cha
UniProt (similar protein)
Q9HVW1
Target protein
VK055_2353

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 648.90 Da
LogP (Crippen) 10.51
H-bond donors 2
H-bond acceptors 6
TPSA 119.36 Ų
Rotatable bonds 34
Aromatic rings 0 / 0
Heavy atoms 44
Fraction sp³ C 0.94
Formula C₃₅H₆₉O₈P

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 119.4
  • −1 ≤ LogP ≤ 5 10.51
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 648.9
  • LogP ≤ 5 10.51
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 34
  • TPSA ≤ 140 Ų 119.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCCCCCCCCCC
InChI 
InChI=1S/C35H69O8P/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-34(36)41-31-33(32-42-44(38,39)40)43-35(37)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h33H,3-32H2,1-2H3,(H2,38,39,40)/t33-/m1/s1
InChIKey 
PORPENFLTBBHSG-MGBGTMOVSA-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
PF02405

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_2353.

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)