Ligand profile

GDX

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

Bound to: KP13_03794 — UDP-glucose 6-dehydrogenase in cps region

Via homolog PDB 1mfz UniProt P11759 Formula C₁₆H₂₃N₅O₁₇P₂
Mol. weight 619.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GDX
PDB
1mfz
UniProt (similar protein)
P11759
Target protein
KP13_03794

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 619.33 Da
LogP (Crippen) -4.54
H-bond donors 10
H-bond acceptors 18
TPSA 348.79 Ų
Rotatable bonds 9
Aromatic rings 2 / 4
Heavy atoms 40
Fraction sp³ C 0.62
Formula C₁₆H₂₃N₅O₁₇P₂

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 348.8
  • −1 ≤ LogP ≤ 5 -4.54
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 619.3
  • LogP ≤ 5 -4.54
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 348.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)C(=O)O)O)O)O)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C16H23N5O17P2/c17-16-19-11-4(12(27)20-16)18-2-21(11)13-8(25)5(22)3(35-13)1-34-39(30,31)38-40(32,33)37-15-9(26)6(23)7(24)10(36-15)14(28)29/h2-3,5-10,13,15,22-26H,1H2,(H,28,29)(H,30,31)(H,32,33)(H3,17,19,20,27)/t3-,5-,6+,7+,8-,9+,10+,13-,15-/m1/s1
InChIKey 
DNBSDUDYNPJVCN-ZXTXFPBHSA-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
PF00984' 'PF03720' 'PF03721

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_03794.

PDB 4

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)