Ligand profile

BYN

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

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

Via homolog PDB 6evd UniProt A2QHE5 Formula C₂₂H₃₁N₄O₁₀P
Mol. weight 542.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BYN
PDB
6evd
UniProt (similar protein)
A2QHE5
Target protein
VK055_3138

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 542.48 Da
LogP (Crippen) -0.13
H-bond donors 8
H-bond acceptors 11
TPSA 220.14 Ų
Rotatable bonds 7
Aromatic rings 2 / 4
Heavy atoms 37
Fraction sp³ C 0.55
Formula C₂₂H₃₁N₄O₁₀P

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 220.1
  • −1 ≤ LogP ≤ 5 -0.13
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 542.5
  • LogP ≤ 5 -0.13
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 220.1
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)N=C(NC4=O)O)O)(C)C
InChI 
InChI=1S/C22H31N4O10P/c1-9-5-11-16-15(10(9)2)22(3,4)6-14(29)26(16)17-19(23-21(32)24-20(17)31)25(11)7-12(27)18(30)13(28)8-36-37(33,34)35/h5,12-14,18,27-30H,6-8H2,1-4H3,(H2,33,34,35)(H2,23,24,31,32)/t12-,13+,14+,18-/m0/s1
InChIKey 
BDNVCRCOZIAGID-LWGWVAHUSA-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)