Ligand profile

API

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

Bound to: KP13_03831 — Succinyl-diaminopimelate desuccinylase

Via homolog PDB 5vo3 UniProt P44514 Formula C₇H₁₄N₂O₄
Mol. weight 190.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
API
PDB
5vo3
UniProt (similar protein)
P44514
Target protein
KP13_03831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 190.20 Da
LogP (Crippen) -1.02
H-bond donors 4
H-bond acceptors 4
TPSA 126.64 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 0.71
Formula C₇H₁₄N₂O₄

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 126.6
  • −1 ≤ LogP ≤ 5 -1.02
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 190.2
  • LogP ≤ 5 -1.02
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 126.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
InChI 
InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5+
InChIKey 
GMKMEZVLHJARHF-SYDPRGILSA-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
PF01546' 'PF07687

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_03831.

PDB 3

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)