Ligand profile

BY9

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

Bound to: KP13_01731 — Ubiquinone/menaquinone biosynthesis methyltransferase ubiE

Via homolog PDB 6uv6 UniProt Q0H2W9 Formula C₂₆H₂₁N₃O₇
Mol. weight 487.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BY9
PDB
6uv6
UniProt (similar protein)
Q0H2W9
Target protein
KP13_01731

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 487.47 Da
LogP (Crippen) 1.29
H-bond donors 6
H-bond acceptors 8
TPSA 157.04 Ų
Rotatable bonds 2
Aromatic rings 5 / 7
Heavy atoms 36
Fraction sp³ C 0.23
Formula C₂₆H₂₁N₃O₇

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 157.0
  • −1 ≤ LogP ≤ 5 1.29
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 487.5
  • LogP ≤ 5 1.29
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 157.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)c3c4c(c5c6ccccc6n(c5c3[nH]2)[C@H]7[C@@H]([C@H]([C@@H]([C@H](O7)CO)O)O)O)C(=O)NC4=O
InChI 
InChI=1S/C26H21N3O7/c30-9-14-21(31)22(32)23(33)26(36-14)29-13-8-4-2-6-11(13)16-18-17(24(34)28-25(18)35)15-10-5-1-3-7-12(10)27-19(15)20(16)29/h1-8,14,21-23,26-27,30-33H,9H2,(H,28,34,35)/t14-,21-,22+,23-,26-/m1/s1
InChIKey 
FAKJOUAYZNXZGV-QCUUGYDUSA-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
PF08241

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_01731.

PDB 7

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)