Ligand profile

JYT

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

Bound to: KP13_02430 — putative inorganic polyphosphate/ATP-NAD kinase

Via homolog PDB 6rbx UniProt Q8Y8D7 Formula C₈H₁₀BrN₅O
Mol. weight 272.11 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JYT
PDB
6rbx
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 272.11 Da
LogP (Crippen) 0.55
H-bond donors 2
H-bond acceptors 6
TPSA 89.85 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 15
Fraction sp³ C 0.38
Formula C₈H₁₀BrN₅O

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 89.8
  • −1 ≤ LogP ≤ 5 0.55
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 272.1
  • LogP ≤ 5 0.55
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 89.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(c(n2)Br)CCCO)N
InChI 
InChI=1S/C8H10BrN5O/c9-8-13-5-6(10)11-4-12-7(5)14(8)2-1-3-15/h4,15H,1-3H2,(H2,10,11,12)
InChIKey 
MUZYIFHIQGFDMZ-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
PF01513' 'PF20143

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_02430.

PDB 51

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

Ligand PDB entry

ChEMBL 3

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)