Ligand profile

LLL

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

Bound to: KP13_31772 — 30S ribosomal protein S12

Via homolog PDB 5obm UniProt P0CX29 Formula C₁₉H₃₉N₅O₇
Mol. weight 449.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LLL
PDB
5obm
UniProt (similar protein)
P0CX29
Target protein
KP13_31772

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 449.55 Da
LogP (Crippen) -3.98
H-bond donors 8
H-bond acceptors 12
TPSA 213.72 Ų
Rotatable bonds 6
Aromatic rings 0 / 3
Heavy atoms 31
Fraction sp³ C 1.00
Formula C₁₉H₃₉N₅O₇

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 213.7
  • −1 ≤ LogP ≤ 5 -3.98
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 449.5
  • LogP ≤ 5 -3.98
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 213.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@@H]3[C@@H](CC[C@H](O3)CN)N)N)N)O
InChI 
InChI=1S/C19H39N5O7/c1-19(27)7-28-18(13(26)16(19)24-2)31-15-11(23)5-10(22)14(12(15)25)30-17-9(21)4-3-8(6-20)29-17/h8-18,24-27H,3-7,20-23H2,1-2H3/t8-,9+,10-,11+,12-,13+,14+,15-,16+,17+,18+,19-/m0/s1
InChIKey 
VEGXETMJINRLTH-BOZYPMBZSA-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' 'PF00252' 'PF00297' 'PF00312' 'PF00572' 'PF00573' 'PF00831' 'PF00832' 'PF01015' 'PF01...

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)