Ligand profile

0JZ

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

Bound to: KP13_04195 — Lipid A export ATP-binding/permease protein msbA

Via homolog PDB 3g60 UniProt P21447 Formula C₂₄H₃₀N₆O₃Se₃
Mol. weight 687.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
0JZ
PDB
3g60
UniProt (similar protein)
P21447
Target protein
KP13_04195

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 687.42 Da
LogP (Crippen) 1.74
H-bond donors 3
H-bond acceptors 6
TPSA 125.97 Ų
Rotatable bonds 3
Aromatic rings 3 / 4
Heavy atoms 36
Fraction sp³ C 0.50
Formula C₂₄H₃₀N₆O₃Se₃

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 126.0
  • −1 ≤ LogP ≤ 5 1.74
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 687.4
  • LogP ≤ 5 1.74
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 126.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@@H]1c2nc(c[se]2)C(=O)N[C@@H](c3nc(c[se]3)C(=O)N[C@@H](c4nc(c[se]4)C(=O)N1)C(C)C)C(C)C
InChI 
InChI=1S/C24H30N6O3Se3/c1-10(2)16-22-25-14(7-34-22)20(32)29-18(12(5)6)24-27-15(9-36-24)21(33)30-17(11(3)4)23-26-13(8-35-23)19(31)28-16/h7-12,16-18H,1-6H3,(H,28,31)(H,29,32)(H,30,33)/t16-,17-,18-/m1/s1
InChIKey 
FWRNUSMIPQTUHH-KZNAEPCWSA-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
PF00664

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_04195.

PDB 5

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

Ligand PDB entry

ChEMBL 3

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)