Ligand profile

4MJ

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

Bound to: VK055_3138 — 3-octaprenyl-4-hydroxybenzoate decarboxylase

Via homolog PDB 4za9 UniProt A2QHE5 Formula C₃₀H₃₇N₄O₁₀P
Mol. weight 644.62 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4MJ
PDB
4za9
UniProt (similar protein)
A2QHE5
Target protein
VK055_3138

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 644.62 Da
LogP (Crippen) 1.32
H-bond donors 7
H-bond acceptors 10
TPSA 216.72 Ų
Rotatable bonds 10
Aromatic rings 3 / 5
Heavy atoms 45
Fraction sp³ C 0.43
Formula C₃₀H₃₇N₄O₁₀P

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 216.7
  • −1 ≤ LogP ≤ 5 1.32
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 644.6
  • LogP ≤ 5 1.32
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 216.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)NC(=O)NC4=O)C(=O)Cc5ccccc5)(C)C
InChI 
InChI=1S/C30H37N4O10P/c1-15-10-18-24-23(16(15)2)30(3,4)12-19(20(35)11-17-8-6-5-7-9-17)34(24)25-27(31-29(40)32-28(25)39)33(18)13-21(36)26(38)22(37)14-44-45(41,42)43/h5-10,19,21-22,26,36-38H,11-14H2,1-4H3,(H2,41,42,43)(H2,31,32,39,40)/t19-,21-,22+,26-/m0/s1
InChIKey 
ONNNUKUOTDQQGL-YPAYRVMASA-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
PF01977' 'PF20696

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_3138.

PDB 21

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)