Ligand profile

J0J

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

Bound to: KP13_01887 — 1,6-anhydro-N-acetylmuramyl-L-alanine amidase ampD

Via homolog PDB 4bol UniProt Q9HT86 Formula C₁₈H₃₁N₅O₉
Mol. weight 461.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
J0J
PDB
4bol
UniProt (similar protein)
Q9HT86
Target protein
KP13_01887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 461.47 Da
LogP (Crippen) -2.66
H-bond donors 8
H-bond acceptors 8
TPSA 251.24 Ų
Rotatable bonds 15
Aromatic rings 0 / 0
Heavy atoms 32
Fraction sp³ C 0.67
Formula C₁₈H₃₁N₅O₉

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 251.2
  • −1 ≤ LogP ≤ 5 -2.66
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 461.5
  • LogP ≤ 5 -2.66
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 251.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=O)O)N)C(=O)N[C@H](C)C(=O)O)C(=O)O)N
InChI 
InChI=1S/C18H31N5O9/c1-8(19)14(25)23-12(18(31)32)6-7-13(24)22-11(5-3-4-10(20)17(29)30)15(26)21-9(2)16(27)28/h8-12H,3-7,19-20H2,1-2H3,(H,21,26)(H,22,24)(H,23,25)(H,27,28)(H,29,30)(H,31,32)/t8-,9-,10-,11+,12-/m1/s1
InChIKey 
VFGFFQOPKZHQLZ-PZWNZHSQSA-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
PF01510

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_01887.

PDB 1

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

Ligand PDB entry

ZINC 46

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

Compound Similarity (Tanimoto)