Ligand profile

K1D

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

Bound to: KP13_09841 — ADP compounds hydrolase nudE

Via homolog PDB 5qjk UniProt Q9UKK9 Formula C₈H₉N₅
Mol. weight 175.19 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
K1D
PDB
5qjk
UniProt (similar protein)
Q9UKK9
Target protein
KP13_09841

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 175.19 Da
LogP (Crippen) 0.56
H-bond donors 1
H-bond acceptors 4
TPSA 57.70 Ų
Rotatable bonds 1
Aromatic rings 2 / 3
Heavy atoms 13
Fraction sp³ C 0.38
Formula C₈H₉N₅

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 57.7
  • −1 ≤ LogP ≤ 5 0.56
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 175.2
  • LogP ≤ 5 0.56
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 57.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1[nH]c2c(n1)c(ncn2)N3CCC3
InChI 
InChI=1S/C8H9N5/c1-2-13(3-1)8-6-7(10-4-9-6)11-5-12-8/h4-5H,1-3H2,(H,9,10,11,12)
InChIKey 
ACPXQMYLXLKGKU-UHFFFAOYSA-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)