Ligand profile

71R

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

Bound to: KP13_18328 — aminoglycoside adenylyltransferase

Via homolog PDB 5lpa UniProt Q8ZPX9 Formula C₂₁H₄₁N₇O₁₂
Mol. weight 583.60 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
71R
PDB
5lpa
UniProt (similar protein)
Q8ZPX9
Target protein
KP13_18328

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 583.60 Da
LogP (Crippen) -7.95
H-bond donors 15
H-bond acceptors 15
TPSA 334.59 Ų
Rotatable bonds 9
Aromatic rings 0 / 3
Heavy atoms 40
Fraction sp³ C 0.90
Formula C₂₁H₄₁N₇O₁₂

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 334.6
  • −1 ≤ LogP ≤ 5 -7.95
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 583.6
  • LogP ≤ 5 -7.95
  • H-bond donors ≤ 5 15
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 334.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C(\N)/N[C@@H]1[C@H]([C@@H]([C@H]([C@@H]([C@H]1O)O)O[C@H]2[C@@H]([C@]([C@@H](O2)C)(CO)O)O[C@H]3[C@H]([C@@H]([C@H]([C@@H](O3)CO)O)O)NC)N/C(=N\[H])/N)O
InChI 
InChI=1S/C21H41N7O12/c1-5-21(36,4-30)16(40-17-9(26-2)13(34)10(31)6(3-29)38-17)18(37-5)39-15-8(28-20(24)25)11(32)7(27-19(22)23)12(33)14(15)35/h5-18,26,29-36H,3-4H2,1-2H3,(H4,22,23,27)(H4,24,25,28)/t5-,6-,7+,8-,9-,10-,11+,12-,13-,14+,15+,16-,17-,18-,21+/m0/s1
InChIKey 
ASXBYYWOLISCLQ-HZYVHMACSA-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
PF01909' 'PF13427

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_18328.

PDB 2

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

Ligand PDB entry

ZINC 21

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)