Ligand profile

DSL

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 5ezm UniProt Q1LDT6 Formula C₅₀H₈₃O₄P
Mol. weight 779.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DSL
PDB
5ezm
UniProt (similar protein)
Q1LDT6
Target protein
VK055_3627

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 779.18 Da
LogP (Crippen) 16.60
H-bond donors 2
H-bond acceptors 2
TPSA 66.76 Ų
Rotatable bonds 30
Aromatic rings 0 / 0
Heavy atoms 55
Fraction sp³ C 0.60
Formula C₅₀H₈₃O₄P

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 16.60
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 779.2
  • LogP ≤ 5 16.60
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Fail
  • Rotatable bonds ≤ 10 30
  • 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\COP(=O)(O)O)/C)/C)/C)/C)/C)/C)/C)/C)/C)C
InChI 
InChI=1S/C50H83O4P/c1-41(2)21-12-22-42(3)23-13-24-43(4)25-14-26-44(5)27-15-28-45(6)29-16-30-46(7)31-17-32-47(8)33-18-34-48(9)35-19-36-49(10)37-20-38-50(11)39-40-54-55(51,52)53/h21,23,25,27,29,31,33,35,37,39H,12-20,22,24,26,28,30,32,34,36,38,40H2,1-11H3,(H2,51,52,53)/b42-23+,43-25-,44-27-,45-29-,46-31-,47-33-,48-35-,49-37-,50-39-
InChIKey 
XBEJBEIXLWRYBT-DJNGBRKISA-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)