Ligand profile

OTP

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

Bound to: VK055_0268 — yceI-like domain protein

Via homolog PDB 1wub UniProt P83815 Formula C₄₀H₆₈O₇P₂
Mol. weight 722.93 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
OTP
PDB
1wub
UniProt (similar protein)
P83815
Target protein
VK055_0268

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 722.93 Da
LogP (Crippen) 13.26
H-bond donors 3
H-bond acceptors 4
TPSA 113.29 Ų
Rotatable bonds 26
Aromatic rings 0 / 0
Heavy atoms 49
Fraction sp³ C 0.60
Formula C₄₀H₆₈O₇P₂

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 113.3
  • −1 ≤ LogP ≤ 5 13.26
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 722.9
  • LogP ≤ 5 13.26
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 26
  • TPSA ≤ 140 Ų 113.3
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/CO[P@](=O)(O)OP(=O)(O)O)/C)/C)/C)/C)/C)/C)/C)C
InChI 
InChI=1S/C40H68O7P2/c1-33(2)17-10-18-34(3)19-11-20-35(4)21-12-22-36(5)23-13-24-37(6)25-14-26-38(7)27-15-28-39(8)29-16-30-40(9)31-32-46-49(44,45)47-48(41,42)43/h17,19,21,23,25,27,29,31H,10-16,18,20,22,24,26,28,30,32H2,1-9H3,(H,44,45)(H2,41,42,43)/b34-19+,35-21+,36-23+,37-25+,38-27+,39-29+,40-31+
InChIKey 
IKKLDISSULFFQO-DJMILUHSSA-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
PF04264

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_0268.

PDB 7

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)