Ligand profile

RPI

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_04222 — ATP-dependent Clp protease ATP-binding subunit clpA

Via homolog PDB 5hbn UniProt P37571 Formula C₆H₁₅N₄O₅P
Mol. weight 254.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RPI
PDB
5hbn
UniProt (similar protein)
P37571
Target protein
KP13_04222

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 254.18 Da
LogP (Crippen) -1.61
H-bond donors 7
H-bond acceptors 4
TPSA 168.76 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.67
Formula C₆H₁₅N₄O₅P

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 168.8
  • −1 ≤ LogP ≤ 5 -1.61
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 254.2
  • LogP ≤ 5 -1.61
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 168.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C(/NCCC[C@@H](C(=O)O)N)\NP(=O)(O)O
InChI 
InChI=1S/C6H15N4O5P/c7-4(5(11)12)2-1-3-9-6(8)10-16(13,14)15/h4H,1-3,7H2,(H,11,12)(H5,8,9,10,13,14,15)/t4-/m0/s1
InChIKey 
CCTIOCVIZPCTGO-BYPYZUCNSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF02861

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_04222.

PDB 6

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)