Ligand profile

NMY

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

Bound to: KP13_02425 — 30S ribosomal protein S16

Via homolog PDB 4lf6 UniProt Q5SJH3 Formula C₂₃H₄₆N₆O₁₃
Mol. weight 614.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NMY
PDB
4lf6
UniProt (similar protein)
Q5SJH3
Target protein
KP13_02425

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 614.65 Da
LogP (Crippen) -8.90
H-bond donors 13
H-bond acceptors 19
TPSA 353.11 Ų
Rotatable bonds 9
Aromatic rings 0 / 4
Heavy atoms 42
Fraction sp³ C 1.00
Formula C₂₃H₄₆N₆O₁₃

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 353.1
  • −1 ≤ LogP ≤ 5 -8.90
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 614.7
  • LogP ≤ 5 -8.90
  • H-bond donors ≤ 5 13
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 353.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CN)O)O)N)O[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O[C@@H]4[C@@H]([C@H]([C@@H]([C@@H](O4)CN)O)O)N)O)O)N
InChI 
InChI=1S/C23H46N6O13/c24-2-7-13(32)15(34)10(28)21(37-7)40-18-6(27)1-5(26)12(31)20(18)42-23-17(36)19(9(4-30)39-23)41-22-11(29)16(35)14(33)8(3-25)38-22/h5-23,30-36H,1-4,24-29H2/t5-,6+,7-,8+,9-,10-,11-,12+,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23+/m1/s1
InChIKey 
PGBHMTALBVVCIT-VCIWKGPPSA-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
PF00163' 'PF00886

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_02425.

PDB 5

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)