Ligand profile

P00

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

Bound to: VK055_3730 — argD

Via homolog PDB 4jew UniProt P40732 Formula C₁₂H₁₈N₃O₈P
Mol. weight 363.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
P00
PDB
4jew
UniProt (similar protein)
P40732
Target protein
VK055_3730

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 363.26 Da
LogP (Crippen) -0.14
H-bond donors 5
H-bond acceptors 8
TPSA 184.79 Ų
Rotatable bonds 9
Aromatic rings 1 / 1
Heavy atoms 24
Fraction sp³ C 0.42
Formula C₁₂H₁₈N₃O₈P

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 184.8
  • −1 ≤ LogP ≤ 5 -0.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 363.3
  • LogP ≤ 5 -0.14
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 184.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/OCC[C@@H](C(=O)O)N)O
InChI 
InChI=1S/C12H18N3O8P/c1-7-11(16)9(5-15-22-3-2-10(13)12(17)18)8(4-14-7)6-23-24(19,20)21/h4-5,10,16H,2-3,6,13H2,1H3,(H,17,18)(H2,19,20,21)/b15-5+/t10-/m0/s1
InChIKey 
HDUKWWSNPJPYAB-XSFFOXFNSA-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
PF00202

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_3730.

PDB 5

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

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)