Ligand profile

ZINC6003711

Virtual-screening candidate from ZINC.

Bound to: KP13_03831 — Succinyl-diaminopimelate desuccinylase

Via homolog UniProt Q96KP4 Formula C₂₄H₃₁N₃O₅
Tanimoto 0.71
Mol. weight 441.53 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC6003711
UniProt (similar protein)
Q96KP4
Tanimoto
0.711
Target protein
KP13_03831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 441.53 Da
LogP (Crippen) 0.87
H-bond donors 5
H-bond acceptors 5
TPSA 141.75 Ų
Rotatable bonds 11
Aromatic rings 2 / 2
Heavy atoms 32
Fraction sp³ C 0.38
Formula C₂₄H₃₁N₃O₅

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 141.7
  • −1 ≤ LogP ≤ 5 0.87
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 441.5
  • LogP ≤ 5 0.87
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 141.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccccc1)C(=O)N[C@@H](Cc1ccccc1)C(=O)O
InChI 
InChI=1S/C24H31N3O5/c1-15(2)20(22(29)26-19(24(31)32)14-17-11-7-4-8-12-17)27-23(30)21(28)18(25)13-16-9-5-3-6-10-16/h3-12,15,18-21,28H,13-14,25H2,1-2H3,(H,26,29)(H,27,30)(H,31,32)/t18-,19+,20+,21+/m1/s1
InChIKey 
GGMURINELPSPEF-ANULTFPQSA-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)