Ligand profile

RRC

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

Bound to: KP13_05165 — Pyridoxamine kinase

Via homolog PDB 1ygk UniProt P82197 Formula C₁₉H₂₆N₆O
Mol. weight 354.46 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RRC
PDB
1ygk
UniProt (similar protein)
P82197
Target protein
KP13_05165

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 354.46 Da
LogP (Crippen) 3.20
H-bond donors 3
H-bond acceptors 7
TPSA 87.89 Ų
Rotatable bonds 8
Aromatic rings 3 / 3
Heavy atoms 26
Fraction sp³ C 0.42
Formula C₁₉H₂₆N₆O

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 87.9
  • −1 ≤ LogP ≤ 5 3.20
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 354.5
  • LogP ≤ 5 3.20
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 87.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@H](CO)Nc1nc(c2c(n1)n(cn2)C(C)C)NCc3ccccc3
InChI 
InChI=1S/C19H26N6O/c1-4-15(11-26)22-19-23-17(20-10-14-8-6-5-7-9-14)16-18(24-19)25(12-21-16)13(2)3/h5-9,12-13,15,26H,4,10-11H2,1-3H3,(H2,20,22,23,24)/t15-/m1/s1
InChIKey 
BTIHMVBBUGXLCJ-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)