Ligand profile

M5Z

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

Bound to: KP13_31772 — 30S ribosomal protein S12

Via homolog PDB 4b3r UniProt Q5SHN3 Formula C₃₂H₅₃N₅O₁₄
Mol. weight 731.80 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
M5Z
PDB
4b3r
UniProt (similar protein)
Q5SHN3
Target protein
KP13_31772

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 731.80 Da
LogP (Crippen) -5.84
H-bond donors 11
H-bond acceptors 19
TPSA 325.32 Ų
Rotatable bonds 11
Aromatic rings 1 / 6
Heavy atoms 51
Fraction sp³ C 0.81
Formula C₃₂H₅₃N₅O₁₄

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 325.3
  • −1 ≤ LogP ≤ 5 -5.84
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 731.8
  • LogP ≤ 5 -5.84
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 325.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)CC[C@@H]2OC[C@@H]3[C@@H](O2)[C@@H]([C@H]([C@H](O3)O[C@@H]4[C@H](C[C@H]([C@@H]([C@H]4O[C@H]5[C@@H]([C@@H]([C@H](O5)CO)O[C@@H]6[C@@H]([C@H]([C@@H]([C@@H](O6)CN)O)O)N)O)O)N)N)N)O
InChI 
InChI=1S/C32H53N5O14/c33-9-15-22(40)23(41)19(36)30(45-15)50-27-16(10-38)46-32(25(27)43)51-29-21(39)13(34)8-14(35)26(29)49-31-20(37)24(42)28-17(47-31)11-44-18(48-28)7-6-12-4-2-1-3-5-12/h1-5,13-32,38-43H,6-11,33-37H2/t13-,14+,15+,16-,17-,18-,19-,20-,21+,22-,23-,24-,25-,26-,27-,28-,29-,30-,31-,32+/m1/s1
InChIKey 
JVOSAEIJIXVWJU-TZWNKDFKSA-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)