Ligand profile

RFL

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

Bound to: VK055_4140 — 2-polyprenyl-6-methoxyphenol 4-hydroxylase

Via homolog PDB 1d7l UniProt P20586 Formula C₂₈H₃₆N₁₀O₁₅P₂
Mol. weight 814.60 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RFL
PDB
1d7l
UniProt (similar protein)
P20586
Target protein
VK055_4140

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 814.60 Da
LogP (Crippen) -2.67
H-bond donors 9
H-bond acceptors 22
TPSA 366.17 Ų
Rotatable bonds 14
Aromatic rings 3 / 6
Heavy atoms 55
Fraction sp³ C 0.46
Formula C₂₈H₃₆N₁₀O₁₅P₂

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 366.2
  • −1 ≤ LogP ≤ 5 -2.67
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 814.6
  • LogP ≤ 5 -2.67
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 22
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 366.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c(cc1N(C)C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
InChI 
InChI=1S/C28H36N10O15P2/c1-11-4-12-14(5-13(11)36(2)3)37(25-19(33-12)26(44)35-28(45)34-25)6-15(39)20(41)16(40)7-50-54(46,47)53-55(48,49)51-8-17-21(42)22(43)27(52-17)38-10-32-18-23(29)30-9-31-24(18)38/h4-5,9-10,15-17,20-22,27,39-43H,6-8H2,1-3H3,(H,46,47)(H,48,49)(H2,29,30,31)(H,35,44,45)/t15-,16+,17+,20-,21+,22+,27+/m0/s1
InChIKey 
UXOZEHHQWXVTPI-MZWSMYJRSA-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_4140.

PDB 11

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

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)