Ligand profile

XBP

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

Bound to: VK055_4831 — HAD hydrolase, IA, variant 3 family protein

Via homolog PDB 4uat UniProt P95649 Formula C₅H₁₂O₁₁P₂
Mol. weight 310.09 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XBP
PDB
4uat
UniProt (similar protein)
P95649
Target protein
VK055_4831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 310.09 Da
LogP (Crippen) -2.50
H-bond donors 6
H-bond acceptors 7
TPSA 191.05 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 18
Fraction sp³ C 0.80
Formula C₅H₁₂O₁₁P₂

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 191.0
  • −1 ≤ LogP ≤ 5 -2.50
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 310.1
  • LogP ≤ 5 -2.50
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 191.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]([C@@H](C(=O)COP(=O)(O)O)O)O)OP(=O)(O)O
InChI 
InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3,5-6,8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,5+/m1/s1
InChIKey 
YAHZABJORDUQGO-WUJLRWPWSA-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
PF00702

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_4831.

PDB 5

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)