Ligand profile

958

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

Bound to: KP13_09841 — ADP compounds hydrolase nudE

Via homolog PDB 5nqr UniProt Q9UKK9 Formula C₁₉H₂₁N₇O₃
Mol. weight 395.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
958
PDB
5nqr
UniProt (similar protein)
Q9UKK9
Target protein
KP13_09841

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 395.42 Da
LogP (Crippen) 0.91
H-bond donors 0
H-bond acceptors 10
TPSA 103.98 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 29
Fraction sp³ C 0.32
Formula C₁₉H₂₁N₇O₃

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 104.0
  • −1 ≤ LogP ≤ 5 0.91
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 395.4
  • LogP ≤ 5 0.91
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 10
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 104.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cccc(c1)c2nnc(o2)Cn3c4c(nc3N(C)C)N(C(=O)N(C4=O)C)C
InChI 
InChI=1S/C19H21N7O3/c1-11-7-6-8-12(9-11)16-22-21-13(29-16)10-26-14-15(20-18(26)23(2)3)24(4)19(28)25(5)17(14)27/h6-9H,10H2,1-5H3
InChIKey 
NHRNLJPTVPQENT-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)