Ligand profile

8GD

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

Bound to: KP13_09841 — ADP compounds hydrolase nudE

Via homolog PDB 3ac9 UniProt Q9UKK9 Formula C₁₀H₁₅N₅O₁₁P₂
Mol. weight 443.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8GD
PDB
3ac9
UniProt (similar protein)
Q9UKK9
Target protein
KP13_09841

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 443.20 Da
LogP (Crippen) -2.13
H-bond donors 7
H-bond acceptors 11
TPSA 252.31 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 28
Fraction sp³ C 0.50
Formula C₁₀H₁₅N₅O₁₁P₂

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 252.3
  • −1 ≤ LogP ≤ 5 -2.13
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 443.2
  • LogP ≤ 5 -2.13
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 252.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=O)CO[P@](=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C10H15N5O11P2/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(25-5)2-24-28(22,23)26-27(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
InChIKey 
LJMLTZSNWOCYNQ-VPENINKCSA-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
PF00293

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_09841.

PDB 53

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

Ligand PDB entry

ChEMBL 5

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

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)