Ligand profile

CHEMBL1164398

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00164 — Bifunctional (p)ppGpp synthase/hydrolase SpoT

Via homolog UniProt Q54089 Formula C₂₂H₄₁N₅O₁₆P₄Si
Mol. weight 783.57 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1164398
UniProt (similar protein)
Q54089
Target protein
KP13_00164

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 783.57 Da
LogP (Crippen) 2.04
H-bond donors 8
H-bond acceptors 13
TPSA 319.25 Ų
Rotatable bonds 14
Aromatic rings 2 / 3
Heavy atoms 48
Fraction sp³ C 0.73
Formula C₂₂H₄₁N₅O₁₆P₄Si

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 319.2
  • −1 ≤ LogP ≤ 5 2.04
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 783.6
  • LogP ≤ 5 2.04
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 319.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)C(=O)Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)CP(=O)(O)O)[C@@H](OP(=O)(O)CP(=O)(O)O)[C@H]2O[Si](C)(C)C(C)(C)C)c(=O)[nH]1
InChI 
InChI=1S/C22H41N5O16P4Si/c1-12(2)18(28)25-21-24-17-14(19(29)26-21)23-9-27(17)20-16(43-48(6,7)22(3,4)5)15(42-47(38,39)11-45(33,34)35)13(41-20)8-40-46(36,37)10-44(30,31)32/h9,12-13,15-16,20H,8,10-11H2,1-7H3,(H,36,37)(H,38,39)(H2,30,31,32)(H2,33,34,35)(H2,24,25,26,28,29)/t13-,15-,16-,20-/m1/s1
InChIKey 
RYFZSVCLZZGIKG-KHTYJDQRSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
ChEMBL
Activity
Active
Curation
pdb_similarity_tanimoto
Binding sites
PF04607' 'PF13328

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_00164.

PDB 5

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

Ligand PDB entry

ChEMBL 6

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)