Ligand profile

MC3

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

Bound to: VK055_3681 — rhomboid family protease GlpG

Via homolog PDB 2xtv UniProt P09391 Formula C₃₆H₇₂NO₈P
Mol. weight 677.94 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MC3
PDB
2xtv
UniProt (similar protein)
P09391
Target protein
VK055_3681

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 677.94 Da
LogP (Crippen) 9.05
H-bond donors 0
H-bond acceptors 8
TPSA 111.19 Ų
Rotatable bonds 34
Aromatic rings 0 / 0
Heavy atoms 46
Fraction sp³ C 0.94
Formula C₃₆H₇₂NO₈P

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 111.2
  • −1 ≤ LogP ≤ 5 9.05
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 677.9
  • LogP ≤ 5 9.05
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 34
  • TPSA ≤ 140 Ų 111.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])OCC[N+](C)(C)C)OC(=O)CCCCCCCCCCCCC
InChI 
InChI=1S/C36H72NO8P/c1-6-8-10-12-14-16-18-20-22-24-26-28-35(38)42-32-34(33-44-46(40,41)43-31-30-37(3,4)5)45-36(39)29-27-25-23-21-19-17-15-13-11-9-7-2/h34H,6-33H2,1-5H3/t34-/m1/s1
InChIKey 
CITHEXJVPOWHKC-UUWRZZSWSA-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
PF01694

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_3681.

PDB 8

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)