Ligand profile

KOY

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

Bound to: VK055_4857 — O-succinylbenzoate-CoA ligase

Via homolog PDB 6nj0 UniProt P37353 Formula C₂₆H₂₅N₅O₇
Mol. weight 519.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KOY
PDB
6nj0
UniProt (similar protein)
P37353
Target protein
VK055_4857

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 519.51 Da
LogP (Crippen) 1.62
H-bond donors 4
H-bond acceptors 11
TPSA 182.91 Ų
Rotatable bonds 9
Aromatic rings 4 / 5
Heavy atoms 38
Fraction sp³ C 0.27
Formula C₂₆H₂₅N₅O₇

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 182.9
  • −1 ≤ LogP ≤ 5 1.62
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 519.5
  • LogP ≤ 5 1.62
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 182.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(c(c1)C(=O)CCc2cccc(c2)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)C(=O)O
InChI 
InChI=1S/C26H25N5O7/c27-23-20-24(29-12-28-23)31(13-30-20)25-22(34)21(33)19(38-25)11-37-15-5-3-4-14(10-15)8-9-18(32)16-6-1-2-7-17(16)26(35)36/h1-7,10,12-13,19,21-22,25,33-34H,8-9,11H2,(H,35,36)(H2,27,28,29)/t19-,21-,22-,25-/m1/s1
InChIKey 
GEMGRSMVWNUQGG-PTGPVQHPSA-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
PF00501

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_4857.

PDB 11

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)