Ligand profile

RFP

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 6brd UniProt F2R776 Formula C₄₃H₅₈N₄O₁₂
Mol. weight 822.95 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
RFP
PDB
6brd
UniProt (similar protein)
F2R776
Target protein
VK055_0339

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 822.95 Da
LogP (Crippen) 4.34
H-bond donors 6
H-bond acceptors 15
TPSA 220.15 Ų
Rotatable bonds 4
Aromatic rings 2 / 6
Heavy atoms 59
Fraction sp³ C 0.53
Formula C₄₃H₅₈N₄O₁₂

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 4.34
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 823.0
  • LogP ≤ 5 4.34
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 220.1
PAINS Alert

Matches PAINS filter: hzone_phenol_A(479). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](C=C\C=C(/C(=O)Nc(c2O)c(c3O)\C=N\N5CCN(CC5)C)\C)C)O)C)O)C)OC(=O)C)C)OC)C)O
InChI 
InChI=1S/C43H58N4O12/c1-21-12-11-13-22(2)42(55)45-33-28(20-44-47-17-15-46(9)16-18-47)37(52)30-31(38(33)53)36(51)26(6)40-32(30)41(54)43(8,59-40)57-19-14-29(56-10)23(3)39(58-27(7)48)25(5)35(50)24(4)34(21)49/h11-14,19-21,23-25,29,34-35,39,49-53H,15-18H2,1-10H3,(H,45,55)/b12-11?,19-14+,22-13-,44-20+/t21-,23+,24+,25+,29-,34-,35+,39+,43-/m0/s1
InChIKey 
JQXXHWHPUNPDRT-MTOCILLGSA-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)