Ligand profile

R78

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_05165 — Pyridoxamine kinase

Via homolog UniProt O00764 Formula C₂₈H₃₉N₇O₃
pchembl 6.41 ~389.0 nM
Mol. weight 521.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
R78
UniProt (similar protein)
O00764
pchembl
6.410 (~389.0 nM)
Target protein
KP13_05165

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 521.67 Da
LogP (Crippen) 3.56
H-bond donors 2
H-bond acceptors 8
TPSA 102.93 Ų
Rotatable bonds 7
Aromatic rings 2 / 5
Heavy atoms 38
Fraction sp³ C 0.57
Formula C₂₈H₃₉N₇O₃

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 102.9
  • −1 ≤ LogP ≤ 5 3.56
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 521.7
  • LogP ≤ 5 3.56
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 102.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@@H]1C(=O)N(c2cnc(nc2N1C3CCCC3)Nc4ccc(cc4OC)C(=O)NC5CCN(CC5)C)C
InChI 
InChI=1S/C28H39N7O3/c1-5-22-27(37)34(3)23-17-29-28(32-25(23)35(22)20-8-6-7-9-20)31-21-11-10-18(16-24(21)38-4)26(36)30-19-12-14-33(2)15-13-19/h10-11,16-17,19-20,22H,5-9,12-15H2,1-4H3,(H,30,36)(H,29,31,32)/t22-/m1/s1
InChIKey 
XQVVPGYIWAGRNI-JOCHJYFZSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
ChEMBL
Activity
Active
Binding sites
PF08543

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_05165.

PDB 13

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

Ligand PDB entry

ChEMBL 4

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)