Ligand profile

RPO

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

Bound to: KP13_31772 — 30S ribosomal protein S12

Via homolog PDB 4b3s UniProt Q5SHN3 Formula C₃₀H₅₁N₅O₁₄
Mol. weight 705.76 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RPO
PDB
4b3s
UniProt (similar protein)
Q5SHN3
Target protein
KP13_31772

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 705.76 Da
LogP (Crippen) -6.64
H-bond donors 12
H-bond acceptors 19
TPSA 336.32 Ų
Rotatable bonds 12
Aromatic rings 1 / 5
Heavy atoms 49
Fraction sp³ C 0.80
Formula C₃₀H₅₁N₅O₁₄

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 336.3
  • −1 ≤ LogP ≤ 5 -6.64
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 705.8
  • LogP ≤ 5 -6.64
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 336.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)CO[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)N)O[C@@H]3[C@H](C[C@H]([C@@H]([C@H]3O[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O[C@@H]5[C@@H]([C@H]([C@@H]([C@@H](O5)CN)O)O)N)O)O)N)N)CO
InChI 
InChI=1S/C30H51N5O14/c31-7-14-20(39)21(40)17(34)28(44-14)48-26-16(9-37)46-30(23(26)42)49-27-19(38)12(32)6-13(33)24(27)47-29-18(35)22(41)25(15(8-36)45-29)43-10-11-4-2-1-3-5-11/h1-5,12-30,36-42H,6-10,31-35H2/t12-,13+,14+,15-,16-,17-,18-,19+,20-,21-,22-,23-,24-,25-,26-,27-,28-,29-,30+/m1/s1
InChIKey 
DRHDMQJFWDZMND-JCNXQQRHSA-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)