Ligand profile

H5P

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

Bound to: VK055_2887 — adenylosuccinate synthase

Via homolog PDB 1juy UniProt P0A7D4 Formula C₇H₁₁N₂O₉P
Mol. weight 298.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
H5P
PDB
1juy
UniProt (similar protein)
P0A7D4
Target protein
VK055_2887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 298.14 Da
LogP (Crippen) -3.25
H-bond donors 6
H-bond acceptors 7
TPSA 174.65 Ų
Rotatable bonds 3
Aromatic rings 0 / 2
Heavy atoms 19
Fraction sp³ C 0.71
Formula C₇H₁₁N₂O₉P

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 174.6
  • −1 ≤ LogP ≤ 5 -3.25
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 298.1
  • LogP ≤ 5 -3.25
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 174.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]1[C@H]([C@H]([C@]2(O1)C(=O)NC(=O)N2)O)O)OP(=O)(O)O
InChI 
InChI=1S/C7H11N2O9P/c10-3-2(1-17-19(14,15)16)18-7(4(3)11)5(12)8-6(13)9-7/h2-4,10-11H,1H2,(H2,14,15,16)(H2,8,9,12,13)/t2-,3-,4-,7+/m1/s1
InChIKey 
HVXIMXHBUJADCC-GTBMBKLPSA-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
PF00709

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_2887.

PDB 14

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)