Ligand profile

LP5

Ligand co-crystallized with this exact protein (Protein Data Bank).

Bound to: VK055_2067 — UDP-2,3-diacylglucosamine hydrolase

Direct evidence PDB 6ph9 UniProt A6T5R0 Formula C₃₄H₆₆NO₁₂P
Mol. weight 711.87 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LP5
PDB
6ph9
UniProt (this protein)
A6T5R0
Target protein
VK055_2067

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 711.87 Da
LogP (Crippen) 4.91
H-bond donors 7
H-bond acceptors 10
TPSA 212.31 Ų
Rotatable bonds 29
Aromatic rings 0 / 1
Heavy atoms 48
Fraction sp³ C 0.94
Formula C₃₄H₆₆NO₁₂P

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 212.3
  • −1 ≤ LogP ≤ 5 4.91
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 711.9
  • LogP ≤ 5 4.91
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 29
  • TPSA ≤ 140 Ų 212.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCC[C@H](CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1OP(=O)(O)O)CO)O)OC(=O)C[C@@H](CCCCCCCCCCC)O)O
InChI 
InChI=1S/C34H66NO12P/c1-3-5-7-9-11-13-15-17-19-21-26(37)23-29(39)35-31-33(32(41)28(25-36)45-34(31)47-48(42,43)44)46-30(40)24-27(38)22-20-18-16-14-12-10-8-6-4-2/h26-28,31-34,36-38,41H,3-25H2,1-2H3,(H,35,39)(H2,42,43,44)/t26-,27-,28-,31-,32-,33-,34-/m1/s1
InChIKey 
HEHQDWUWJVPREQ-XQJZMFRCSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00149

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_2067.

PDB 1

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)