Ligand profile

CHEMBL1163568

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt Q54089 Formula C₁₂H₂₁N₅O₁₅P₄
Mol. weight 599.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1163568
UniProt (similar protein)
Q54089
Target protein
KP13_00164

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 599.22 Da
LogP (Crippen) -2.00
H-bond donors 9
H-bond acceptors 13
TPSA 327.17 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 36
Fraction sp³ C 0.58
Formula C₁₂H₂₁N₅O₁₅P₄

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 327.2
  • −1 ≤ LogP ≤ 5 -2.00
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 599.2
  • LogP ≤ 5 -2.00
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 327.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
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)c(=O)[nH]1
InChI 
InChI=1S/C12H21N5O15P4/c13-12-15-9-6(10(19)16-12)14-2-17(9)11-7(18)8(32-36(28,29)4-34(23,24)25)5(31-11)1-30-35(26,27)3-33(20,21)22/h2,5,7-8,11,18H,1,3-4H2,(H,26,27)(H,28,29)(H2,20,21,22)(H2,23,24,25)(H3,13,15,16,19)/t5-,7-,8-,11-/m1/s1
InChIKey 
IKUGYHZNNUDHFA-IOSLPCCCSA-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)