Ligand profile

CHEMBL5280439

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_02200 — Isopentenyl-diphosphate Delta-isomerase

Via homolog UniProt Q46822 Formula C₄H₁₃N₃O₅P₂
pchembl 6.89 ~128.8 nM
Mol. weight 245.11 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5280439
UniProt (similar protein)
Q46822
pchembl
6.890 (~128.8 nM)
Target protein
KP13_02200

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 245.11 Da
LogP (Crippen) -1.12
H-bond donors 6
H-bond acceptors 3
TPSA 156.73 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 0.75
Formula C₄H₁₃N₃O₅P₂

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 156.7
  • −1 ≤ LogP ≤ 5 -1.12
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 245.1
  • LogP ≤ 5 -1.12
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 3
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 156.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N=C(N)NCCP(=O)(O)CP(=O)(O)O
InChI 
InChI=1S/C4H13N3O5P2/c5-4(6)7-1-2-13(8,9)3-14(10,11)12/h1-3H2,(H,8,9)(H4,5,6,7)(H2,10,11,12)
InChIKey 
MNWZTJZEYHDOIP-UHFFFAOYSA-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
Binding sites
PF00293

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_02200.

PDB 8

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

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 7

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

Compound Similarity (Tanimoto)