Ligand profile

ZINC12504508

Virtual-screening candidate from ZINC.

Bound to: KP13_05165 — Pyridoxamine kinase

Via homolog UniProt P82197 Formula C₂₀H₂₈N₆O
Tanimoto 1.00
Mol. weight 368.49 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12504508
UniProt (similar protein)
P82197
Tanimoto
1.000
Target protein
KP13_05165

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 368.49 Da
LogP (Crippen) 3.23
H-bond donors 2
H-bond acceptors 7
TPSA 79.10 Ų
Rotatable bonds 8
Aromatic rings 3 / 3
Heavy atoms 27
Fraction sp³ C 0.45
Formula C₂₀H₂₈N₆O

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 79.1
  • −1 ≤ LogP ≤ 5 3.23
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 368.5
  • LogP ≤ 5 3.23
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 79.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@H](CO)Nc1nc(N(C)Cc2ccccc2)c2ncn(C(C)C)c2n1
InChI 
InChI=1S/C20H28N6O/c1-5-16(12-27)22-20-23-18(25(4)11-15-9-7-6-8-10-15)17-19(24-20)26(13-21-17)14(2)3/h6-10,13-14,16,27H,5,11-12H2,1-4H3,(H,22,23,24)/t16-/m1/s1
InChIKey 
YPYWONAECUVKHY-MRXNPFEDSA-N

Provenance

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

Method
LigQ nearest_k
Query
RMC
Homolog
P82197

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 5

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)