Ligand profile

5TR

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

Bound to: VK055_3627 — 4-amino-4-deoxy-L-arabinose (L-Ara4N) transferase

Via homolog PDB 5f15 UniProt Q1LDT6 Formula C₅₅H₉₁O₄P
Mol. weight 847.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5TR
PDB
5f15
UniProt (similar protein)
Q1LDT6
Target protein
VK055_3627

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 847.30 Da
LogP (Crippen) 18.33
H-bond donors 2
H-bond acceptors 2
TPSA 66.76 Ų
Rotatable bonds 33
Aromatic rings 0 / 0
Heavy atoms 60
Fraction sp³ C 0.60
Formula C₅₅H₉₁O₄P

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 66.8
  • −1 ≤ LogP ≤ 5 18.33
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 847.3
  • LogP ≤ 5 18.33
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Fail
  • Rotatable bonds ≤ 10 33
  • TPSA ≤ 140 Ų 66.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=CCC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C\CC/C(=C/CC/C(=C\CC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C/COP(=O)(O)O)/C)/C)/C)/C)/C)/C)/C)/C)/C)/C)C
InChI 
InChI=1S/C55H91O4P/c1-45(2)23-13-24-46(3)25-14-26-47(4)27-15-28-48(5)29-16-30-49(6)31-17-32-50(7)33-18-34-51(8)35-19-36-52(9)37-20-38-53(10)39-21-40-54(11)41-22-42-55(12)43-44-59-60(56,57)58/h23,25,27,29,31,33,35,37,39,41,43H,13-22,24,26,28,30,32,34,36,38,40,42,44H2,1-12H3,(H2,56,57,58)/b46-25+,47-27+,48-29+,49-31-,50-33+,51-35-,52-37+,53-39+,54-41+,55-43+
InChIKey 
UFPHFKCTOZIAFY-ZUPWODLNSA-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
PF13231

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_3627.

PDB 3

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)