Ligand profile

H2U

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

Bound to: VK055_1764 — galactose-1-phosphate uridylyltransferase

Via homolog PDB 6gqd UniProt P07902-2 Formula C₉H₁₅N₂O₉P
Mol. weight 326.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
H2U
PDB
6gqd
UniProt (similar protein)
P07902-2
Target protein
VK055_1764

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 326.20 Da
LogP (Crippen) -2.52
H-bond donors 5
H-bond acceptors 7
TPSA 165.86 Ų
Rotatable bonds 4
Aromatic rings 0 / 2
Heavy atoms 21
Fraction sp³ C 0.78
Formula C₉H₁₅N₂O₉P

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 165.9
  • −1 ≤ LogP ≤ 5 -2.52
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 326.2
  • LogP ≤ 5 -2.52
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 165.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
InChI 
InChI=1S/C9H15N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h4,6-8,13-14H,1-3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKey 
NBWDKGJHOHJBRJ-XVFCMESISA-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
PF01087

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_1764.

PDB 3

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)