Ligand profile

BYC

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

Bound to: VK055_1041 — phenylacetic acid catabolic family protein

Via homolog PDB 3pvr UniProt P76077 Formula C₂₈H₄₀N₇O₁₇P₃S
Mol. weight 871.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BYC
PDB
3pvr
UniProt (similar protein)
P76077
Target protein
VK055_1041

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 871.65 Da
LogP (Crippen) -0.02
H-bond donors 9
H-bond acceptors 19
TPSA 363.63 Ų
Rotatable bonds 20
Aromatic rings 3 / 4
Heavy atoms 56
Fraction sp³ C 0.50
Formula C₂₈H₄₀N₇O₁₇P₃S

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 363.6
  • −1 ≤ LogP ≤ 5 -0.02
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 871.6
  • LogP ≤ 5 -0.02
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 363.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)c4ccccc4)O
InChI 
InChI=1S/C28H40N7O17P3S/c1-28(2,22(38)25(39)31-9-8-18(36)30-10-11-56-27(40)16-6-4-3-5-7-16)13-49-55(46,47)52-54(44,45)48-12-17-21(51-53(41,42)43)20(37)26(50-17)35-15-34-19-23(29)32-14-33-24(19)35/h3-7,14-15,17,20-22,26,37-38H,8-13H2,1-2H3,(H,30,36)(H,31,39)(H,44,45)(H,46,47)(H2,29,32,33)(H2,41,42,43)/t17-,20-,21-,22+,26-/m1/s1
InChIKey 
VEVJTUNLALKRNO-TYHXJLICSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF05138

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_1041.

PDB 2

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 4

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)