Ligand profile

AM2

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

Bound to: KP13_31772 — 30S ribosomal protein S12

Via homolog PDB 4aqy UniProt Q5SHN3 Formula C₂₁H₄₁N₅O₁₁
Mol. weight 539.58 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AM2
PDB
4aqy
UniProt (similar protein)
Q5SHN3
Target protein
KP13_31772

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 539.58 Da
LogP (Crippen) -6.95
H-bond donors 11
H-bond acceptors 16
TPSA 283.64 Ų
Rotatable bonds 6
Aromatic rings 0 / 4
Heavy atoms 37
Fraction sp³ C 1.00
Formula C₂₁H₄₁N₅O₁₁

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 283.6
  • −1 ≤ LogP ≤ 5 -6.95
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 539.6
  • LogP ≤ 5 -6.95
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 283.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN[C@H]1[C@H]([C@@H]2[C@H](C[C@H]([C@H](O2)O[C@@H]3[C@H](C[C@H]([C@@H]([C@H]3O)O)N)N)N)O[C@@H]1O[C@@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)N)O)O)O
InChI 
InChI=1S/C21H41N5O11/c1-26-11-14(30)18-8(33-20(11)37-21-16(32)13(29)10(25)9(4-27)34-21)3-7(24)19(36-18)35-17-6(23)2-5(22)12(28)15(17)31/h5-21,26-32H,2-4,22-25H2,1H3/t5-,6+,7-,8+,9-,10-,11+,12+,13+,14-,15-,16-,17-,18+,19+,20-,21-/m1/s1
InChIKey 
XZNUGFQTQHRASN-XQENGBIVSA-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
PF00164

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_31772.

PDB 12

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

Ligand PDB entry

ChEMBL 2

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)