Ligand profile

ZINC5113891

Virtual-screening candidate from ZINC.

Bound to: KP13_03824 — Dihydrodipicolinate synthase

Via homolog UniProt D0CFC3 Formula C₁₂H₂₅N₃O₆
Tanimoto 0.63
Mol. weight 307.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5113891
UniProt (similar protein)
D0CFC3
Tanimoto
0.630
Target protein
KP13_03824

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 307.35 Da
LogP (Crippen) -2.32
H-bond donors 7
H-bond acceptors 7
TPSA 179.13 Ų
Rotatable bonds 12
Aromatic rings 0 / 0
Heavy atoms 21
Fraction sp³ C 0.83
Formula C₁₂H₂₅N₃O₆

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 179.1
  • −1 ≤ LogP ≤ 5 -2.32
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 307.3
  • LogP ≤ 5 -2.32
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 179.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@@H](CC[C@@H](O)CNC[C@H](O)CC[C@H](N)C(=O)O)C(=O)O
InChI 
InChI=1S/C12H25N3O6/c13-9(11(18)19)3-1-7(16)5-15-6-8(17)2-4-10(14)12(20)21/h7-10,15-17H,1-6,13-14H2,(H,18,19)(H,20,21)/t7-,8-,9+,10+/m1/s1
InChIKey 
COYAOJMPFAKKAM-IMSYWVGJSA-N

Provenance

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

Method
LigQ nearest_k
Query
LYZ
Homolog
D0CFC3

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_03824.

PDB 7

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

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

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

Compound Similarity (Tanimoto)