Ligand profile

CHEMBL1163576

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt Q54089 Formula C₁₂H₂₁N₅O₁₄P₄
Mol. weight 583.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1163576
UniProt (similar protein)
Q54089
Target protein
KP13_00164

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 583.22 Da
LogP (Crippen) -0.97
H-bond donors 8
H-bond acceptors 12
TPSA 306.94 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 35
Fraction sp³ C 0.58
Formula C₁₂H₂₁N₅O₁₄P₄

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 306.9
  • −1 ≤ LogP ≤ 5 -0.97
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 583.2
  • LogP ≤ 5 -0.97
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 306.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(ncn2[C@H]2C[C@H](OP(=O)(O)CP(=O)(O)O)[C@@H](COP(=O)(O)CP(=O)(O)O)O2)c(=O)[nH]1
InChI 
InChI=1S/C12H21N5O14P4/c13-12-15-10-9(11(18)16-12)14-3-17(10)8-1-6(31-35(27,28)5-33(22,23)24)7(30-8)2-29-34(25,26)4-32(19,20)21/h3,6-8H,1-2,4-5H2,(H,25,26)(H,27,28)(H2,19,20,21)(H2,22,23,24)(H3,13,15,16,18)/t6-,7+,8+/m0/s1
InChIKey 
FBKHAJAKIHOGTN-XLPZGREQSA-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)