Ligand profile

ZINC5706877

Virtual-screening candidate from ZINC.

Bound to: VK055_1234 — succinylarginine dihydrolase

Via homolog UniProt P76216 Formula C₁₂H₂₆N₈O₃
Tanimoto 0.62
Mol. weight 330.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5706877
UniProt (similar protein)
P76216
Tanimoto
0.625
Target protein
VK055_1234

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 330.39 Da
LogP (Crippen) -2.59
H-bond donors 9
H-bond acceptors 5
TPSA 216.22 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 23
Fraction sp³ C 0.67
Formula C₁₂H₂₆N₈O₃

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 216.2
  • −1 ≤ LogP ≤ 5 -2.59
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 330.4
  • LogP ≤ 5 -2.59
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 216.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N=C(N)NCCC[C@H](N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)O
InChI 
InChI=1S/C12H26N8O3/c13-7(3-1-5-18-11(14)15)9(21)20-8(10(22)23)4-2-6-19-12(16)17/h7-8H,1-6,13H2,(H,20,21)(H,22,23)(H4,14,15,18)(H4,16,17,19)/t7-,8-/m0/s1
InChIKey 
OMLWNBVRVJYMBQ-YUMQZZPRSA-N

Provenance

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

Method
LigQ nearest_k
Query
SUG
Homolog
P76216

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_1234.

PDB 2

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)