Ligand profile

ZINC4899773

Virtual-screening candidate from ZINC.

Bound to: KP13_03831 — Succinyl-diaminopimelate desuccinylase

Via homolog UniProt Q96KP4 Formula C₂₁H₃₃N₃O₄
Tanimoto 0.68
Mol. weight 391.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4899773
UniProt (similar protein)
Q96KP4
Tanimoto
0.682
Target protein
KP13_03831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 391.51 Da
LogP (Crippen) 1.70
H-bond donors 4
H-bond acceptors 4
TPSA 121.52 Ų
Rotatable bonds 11
Aromatic rings 1 / 1
Heavy atoms 28
Fraction sp³ C 0.57
Formula C₂₁H₃₃N₃O₄

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 121.5
  • −1 ≤ LogP ≤ 5 1.70
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 391.5
  • LogP ≤ 5 1.70
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 121.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)C[C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(=O)O
InChI 
InChI=1S/C21H33N3O4/c1-13(2)10-16(22)19(25)23-17(11-14(3)4)20(26)24-18(21(27)28)12-15-8-6-5-7-9-15/h5-9,13-14,16-18H,10-12,22H2,1-4H3,(H,23,25)(H,24,26)(H,27,28)/t16-,17-,18-/m0/s1
InChIKey 
UBZGNBKMIJHOHL-BZSNNMDCSA-N

Provenance

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

Method
LigQ nearest_k
Query
BES
Homolog
Q96KP4

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 4

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)