Ligand profile

R9A

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

Bound to: VK055_1043 — primary amine oxidase

Via homolog PDB 2cg0 UniProt P46881 Formula C₄₉H₆₉N₇ORu
Mol. weight 873.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
R9A
PDB
2cg0
UniProt (similar protein)
P46881
Target protein
VK055_1043

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 873.21 Da
LogP (Crippen) 8.50
H-bond donors 0
H-bond acceptors 8
TPSA 31.91 Ų
Rotatable bonds 12
Aromatic rings 2 / 11
Heavy atoms 58
Fraction sp³ C 0.59
Formula C₄₉H₆₉N₇ORu

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 31.9
  • −1 ≤ LogP ≤ 5 8.50
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 873.2
  • LogP ≤ 5 8.50
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 31.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C)c1cccc(c1)OCCCCCCCCCC2=C3C=CC4=CC=CN5C4=C3N([Ru]567(N8CCCCC8C9N6CCCC9)N1CCCCC1C1N7CCC=C1)C=C2
InChI 
InChI=1S/C29H35N3O.C10H18N2.C10H16N2.Ru/c1-32(2)25-14-10-15-26(22-25)33-21-9-7-5-3-4-6-8-12-23-18-20-31-29-27(23)17-16-24-13-11-19-30-28(24)29;2*1-3-7-11-9(5-1)10-6-2-4-8-12-10;/h10-11,13-20,22H,3-9,12,21H2,1-2H3;9-10H,1-8H2;1,5,9-10H,2-4,6-8H2;/q3*-2;+6
InChIKey 
KSZLCAAYKNWBHP-UHFFFAOYSA-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
PF01179

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_1043.

PDB 14

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

Ligand PDB entry

ChEMBL 9

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)