Ligand profile

6DB

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

Bound to: KP13_01017 — Lysine-arginine-ornithine-binding periplasmic protein

Via homolog PDB 5ito UniProt P35120 Formula C₉H₁₈N₄O₄
Mol. weight 246.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6DB
PDB
5ito
UniProt (similar protein)
P35120
Target protein
KP13_01017

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 246.27 Da
LogP (Crippen) -1.23
H-bond donors 6
H-bond acceptors 4
TPSA 148.53 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 17
Fraction sp³ C 0.67
Formula C₉H₁₈N₄O₄

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 148.5
  • −1 ≤ LogP ≤ 5 -1.23
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 246.3
  • LogP ≤ 5 -1.23
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 148.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](C)C(=O)O
InChI 
InChI=1S/C9H18N4O4/c1-5(7(14)15)13-6(8(16)17)3-2-4-12-9(10)11/h5-6,13H,2-4H2,1H3,(H,14,15)(H,16,17)(H4,10,11,12)/t5-,6+/m1/s1
InChIKey 
IMXSCCDUAFEIOE-RITPCOANSA-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
PF00497

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_01017.

PDB 7

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)