Ligand profile

OPK

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

Bound to: VK055_2050 — yjdL peptide transporter

Via homolog PDB 7q0m UniProt A0A2R9TD79 Formula C₁₉H₂₈N₄O₇
Mol. weight 424.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
OPK
PDB
7q0m
UniProt (similar protein)
A0A2R9TD79
Target protein
VK055_2050

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 424.45 Da
LogP (Crippen) 1.54
H-bond donors 4
H-bond acceptors 7
TPSA 173.89 Ų
Rotatable bonds 12
Aromatic rings 1 / 1
Heavy atoms 30
Fraction sp³ C 0.53
Formula C₁₉H₂₈N₄O₇

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 173.9
  • −1 ≤ LogP ≤ 5 1.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 424.5
  • LogP ≤ 5 1.54
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 173.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@@H](C(=O)O)NC(=O)[C@H](CCCCNC(=O)OCc1ccc(cc1)[N+](=O)[O-])N
InChI 
InChI=1S/C19H28N4O7/c1-12(2)16(18(25)26)22-17(24)15(20)5-3-4-10-21-19(27)30-11-13-6-8-14(9-7-13)23(28)29/h6-9,12,15-16H,3-5,10-11,20H2,1-2H3,(H,21,27)(H,22,24)(H,25,26)/t15-,16-/m0/s1
InChIKey 
TZRRFQDYTMZNQR-HOTGVXAUSA-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
PF00854

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_2050.

PDB 13

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)