Ligand profile

R6C

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

Bound to: KP13_05165 — Pyridoxamine kinase

Via homolog PDB 1yhj UniProt P82197 Formula C₁₉H₂₅N₅O₂
Mol. weight 355.44 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
R6C
PDB
1yhj
UniProt (similar protein)
P82197
Target protein
KP13_05165

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 355.44 Da
LogP (Crippen) 3.17
H-bond donors 2
H-bond acceptors 7
TPSA 85.09 Ų
Rotatable bonds 8
Aromatic rings 3 / 3
Heavy atoms 26
Fraction sp³ C 0.42
Formula C₁₉H₂₅N₅O₂

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 85.1
  • −1 ≤ LogP ≤ 5 3.17
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 355.4
  • LogP ≤ 5 3.17
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 85.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@H](CO)Nc1nc2c(c(n1)OCc3ccccc3)ncn2C(C)C
InChI 
InChI=1S/C19H25N5O2/c1-4-15(10-25)21-19-22-17-16(20-12-24(17)13(2)3)18(23-19)26-11-14-8-6-5-7-9-14/h5-9,12-13,15,25H,4,10-11H2,1-3H3,(H,21,22,23)/t15-/m1/s1
InChIKey 
HGADNQLEUZSUEJ-OAHLLOKOSA-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
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 12

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)