Ligand profile

JRN

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

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

Via homolog PDB 6r3i UniProt A2QHE5 Formula C₃₀H₃₄F₅N₄O₉P²⁺
Mol. weight 720.59 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JRN
PDB
6r3i
UniProt (similar protein)
A2QHE5
Target protein
VK055_3138

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 720.59 Da
LogP (Crippen) 1.30
H-bond donors 7
H-bond acceptors 7
TPSA 200.93 Ų
Rotatable bonds 10
Aromatic rings 4 / 5
Heavy atoms 49
Fraction sp³ C 0.47
Formula C₃₀H₃₄F₅N₄O₉P²⁺

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 200.9
  • −1 ≤ LogP ≤ 5 1.30
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 720.6
  • LogP ≤ 5 1.30
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 200.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c3c(c1C)C(C[C@H]([n+]3c4c([n+]2C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)NC(=O)NC4=O)CCc5c(c(c(c(c5F)F)F)F)F)(C)C
InChI 
InChI=1S/C30H32F5N4O9P/c1-11-7-15-24-18(12(11)2)30(3,4)8-13(5-6-14-19(31)21(33)23(35)22(34)20(14)32)39(24)25-27(36-29(44)37-28(25)43)38(15)9-16(40)26(42)17(41)10-48-49(45,46)47/h7,13,16-17,26,40-42H,5-6,8-10H2,1-4H3,(H2-,37,43,44,45,46,47)/p+2/t13-,16+,17-,26+/m1/s1
InChIKey 
FIWWNQSCRCYESI-SZRLCVSRSA-P

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)