Ligand profile

PM0

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

Bound to: VK055_0339 — 3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase

Via homolog PDB 4k5s UniProt Q194P4 Formula C₅₃H₇₂O₂₄
Mol. weight 1093.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PM0
PDB
4k5s
UniProt (similar protein)
Q194P4
Target protein
VK055_0339

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1093.14 Da
LogP (Crippen) 0.79
H-bond donors 10
H-bond acceptors 24
TPSA 355.04 Ų
Rotatable bonds 12
Aromatic rings 2 / 9
Heavy atoms 77
Fraction sp³ C 0.72
Formula C₅₃H₇₂O₂₄

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 355.0
  • −1 ≤ LogP ≤ 5 0.79
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1093.1
  • LogP ≤ 5 0.79
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 24
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 355.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(cc2cc3c(c(c2c1O)O)C(=O)[C@]4([C@@H](C3)[C@@H](C(=C(C4=O)C(=O)C)O)OC)O[C@H]5C[C@H]([C@@H]([C@H](O5)C)O)O[C@H]6C[C@H]([C@H]([C@H](O6)C)O)O[C@H]7C[C@]([C@@H]([C@H](O7)C)O)(C)O)O[C@H]8C[C@H]([C@@H]([C@H](O8)C)O)O[C@H]9C[C@H]([C@@H]([C@H](O9)C)O)O
InChI 
InChI=1S/C53H72O24/c1-18-29(73-34-14-30(43(58)21(4)69-34)74-33-13-28(55)42(57)20(3)68-33)12-26-10-25-11-27-48(67-9)47(62)38(19(2)54)50(64)53(27,51(65)40(25)46(61)39(26)41(18)56)77-36-16-32(45(60)23(6)71-36)75-35-15-31(44(59)22(5)70-35)76-37-17-52(8,66)49(63)24(7)72-37/h10,12,20-24,27-28,30-37,42-45,48-49,55-63,66H,11,13-17H2,1-9H3/t20-,21-,22-,23-,24-,27+,28-,30-,31-,32-,33+,34+,35+,36+,37+,42-,43-,44+,45-,48+,49-,52+,53-/m1/s1
InChIKey 
HCTADUCAPFYREF-OFWAWROCSA-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
PF01494

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_0339.

PDB 4

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

Ligand PDB entry

ZINC 22

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

Compound Similarity (Tanimoto)