Ligand profile

CHEMBL1163519

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt P0AG20 Formula C₁₁H₁₇N₅O₉P₂
Mol. weight 425.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1163519
UniProt (similar protein)
P0AG20
Target protein
KP13_00164

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 425.23 Da
LogP (Crippen) -1.31
H-bond donors 6
H-bond acceptors 10
TPSA 223.11 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 27
Fraction sp³ C 0.55
Formula C₁₁H₁₇N₅O₉P₂

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 223.1
  • −1 ≤ LogP ≤ 5 -1.31
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 425.2
  • LogP ≤ 5 -1.31
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 223.1
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](CO)O2)c(=O)[nH]1
InChI 
InChI=1S/C11H17N5O9P2/c12-11-14-9-8(10(18)15-11)13-3-16(9)7-1-5(6(2-17)24-7)25-27(22,23)4-26(19,20)21/h3,5-7,17H,1-2,4H2,(H,22,23)(H2,19,20,21)(H3,12,14,15,18)/t5-,6+,7+/m0/s1
InChIKey 
ZVZSJMNDOXYTME-RRKCRQDMSA-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)