Ligand profile

8DD

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

Bound to: KP13_09841 — ADP compounds hydrolase nudE

Via homolog PDB 3aca UniProt Q9UKK9 Formula C₁₀H₁₅N₅O₁₀P₂
Mol. weight 427.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8DD
PDB
3aca
UniProt (similar protein)
Q9UKK9
Target protein
KP13_09841

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 427.20 Da
LogP (Crippen) -1.42
H-bond donors 6
H-bond acceptors 11
TPSA 232.34 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 27
Fraction sp³ C 0.50
Formula C₁₀H₁₅N₅O₁₀P₂

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 232.3
  • −1 ≤ LogP ≤ 5 -1.42
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 427.2
  • LogP ≤ 5 -1.42
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 232.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)N(C(=O)N2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)N
InChI 
InChI=1S/C10H15N5O10P2/c11-8-7-9(13-3-12-8)15(10(17)14-7)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,14,17)(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,5+,6+/m0/s1
InChIKey 
FEPFWQCDWZFLGY-KVQBGUIXSA-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)