Ligand profile

GXP

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

Bound to: KP13_01654 — Dihydrodipicolinate synthase

Via homolog PDB 4oe7 UniProt P75682 Formula C₅H₆O₅
Mol. weight 146.10 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GXP
PDB
4oe7
UniProt (similar protein)
P75682
Target protein
KP13_01654

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 146.10 Da
LogP (Crippen) -1.41
H-bond donors 2
H-bond acceptors 4
TPSA 91.67 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 10
Fraction sp³ C 0.40
Formula C₅H₆O₅

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 91.7
  • −1 ≤ LogP ≤ 5 -1.41
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 146.1
  • LogP ≤ 5 -1.41
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 91.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H](C=O)O)C(=O)C(=O)O
InChI 
InChI=1S/C5H6O5/c6-2-3(7)1-4(8)5(9)10/h2-3,7H,1H2,(H,9,10)/t3-/m0/s1
InChIKey 
QZKCWTOLHHFWCD-VKHMYHEASA-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
PF00701

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_01654.

PDB 10

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)