Ligand profile

RFH

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 6c7s UniProt Q5YTV5 Formula C₄₃H₅₈N₄O₁₃
Mol. weight 838.95 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
RFH
PDB
6c7s
UniProt (similar protein)
Q5YTV5
Target protein
VK055_0339

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 838.95 Da
LogP (Crippen) 3.15
H-bond donors 5
H-bond acceptors 16
TPSA 248.05 Ų
Rotatable bonds 17
Aromatic rings 1 / 4
Heavy atoms 60
Fraction sp³ C 0.53
Formula C₄₃H₅₈N₄O₁₃

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 248.0
  • −1 ≤ LogP ≤ 5 3.15
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 839.0
  • LogP ≤ 5 3.15
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 17
  • TPSA ≤ 140 Ų 248.0
PAINS Alert

Matches PAINS filter: quinone_A(370). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c2c(c3c1O[C@](C3=O)(C)O/C=C/[C@@H]([C@@H](C)[C@H]([C@H](C)[C@@H]([C@H](C)[C@H]([C@@H](C)/C=C/C=C(\C)/C(=O)N)O)O)OC(=O)C)OC)C(=O)C(=C(C2=O)O)C=NN4CCN(CC4)C)O
InChI 
InChI=1S/C43H58N4O13/c1-21(12-11-13-22(2)42(44)56)33(49)24(4)34(50)25(5)39(59-27(7)48)23(3)29(57-10)14-19-58-43(8)41(55)32-30-31(35(51)26(6)40(32)60-43)38(54)37(53)28(36(30)52)20-45-47-17-15-46(9)16-18-47/h11-14,19-21,23-25,29,33-34,39,49-51,53H,15-18H2,1-10H3,(H2,44,56)/b12-11+,19-14+,22-13+,45-20?/t21-,23+,24+,25+,29-,33-,34+,39+,43-/m0/s1
InChIKey 
ABIUUBSHMGGSQA-AHBFAVFZSA-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)