Ligand profile

FSD

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

Bound to: KP13_00750 — 50S ribosomal protein L4

Via homolog PDB 6czr UniProt Q5SHN9 Formula C₂₉H₄₂N₆O₉
Mol. weight 618.69 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
FSD
PDB
6czr
UniProt (similar protein)
Q5SHN9
Target protein
KP13_00750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 618.69 Da
LogP (Crippen) -0.38
H-bond donors 6
H-bond acceptors 13
TPSA 210.73 Ų
Rotatable bonds 9
Aromatic rings 2 / 4
Heavy atoms 44
Fraction sp³ C 0.59
Formula C₂₉H₄₂N₆O₉

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 210.7
  • −1 ≤ LogP ≤ 5 -0.38
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 618.7
  • LogP ≤ 5 -0.38
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 210.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1[C@H](CC[C@@H](O1)N2C=CC(=NC2=O)NC(=O)c3ccc(cc3)NC(=O)[C@](C)(CO)N)O[C@@H]4[C@@H]([C@H]([C@@H]([C@H](O4)C)N(C)C)O)O
InChI 
InChI=1S/C29H42N6O9/c1-15-19(44-26-24(38)23(37)22(34(4)5)16(2)43-26)10-11-21(42-15)35-13-12-20(33-28(35)41)32-25(39)17-6-8-18(9-7-17)31-27(40)29(3,30)14-36/h6-9,12-13,15-16,19,21-24,26,36-38H,10-11,14,30H2,1-5H3,(H,31,40)(H,32,33,39,41)/t15-,16-,19+,21-,22-,23+,24-,26-,29+/m1/s1
InChIKey 
HDNVYHWHCVTDIV-ZENIWSRCSA-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
PF00252

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_00750.

PDB 6

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)