Ligand profile

7D7

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

Bound to: KP13_00998 — hypothetical protein

Via homolog PDB 5tk9 UniProt O24769 Formula C₁₀H₁₃N₅O₃
Mol. weight 251.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7D7
PDB
5tk9
UniProt (similar protein)
O24769
Target protein
KP13_00998

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 251.25 Da
LogP (Crippen) -1.09
H-bond donors 3
H-bond acceptors 8
TPSA 119.31 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 18
Fraction sp³ C 0.50
Formula C₁₀H₁₃N₅O₃

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 119.3
  • −1 ≤ LogP ≤ 5 -1.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 251.2
  • LogP ≤ 5 -1.09
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 119.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](O3)CO)CO)N
InChI 
InChI=1S/C10H13N5O3/c11-8-7-9(13-3-12-8)15(4-14-7)10-5(1-16)6(2-17)18-10/h3-6,10,16-17H,1-2H2,(H2,11,12,13)/t5-,6-,10-/m1/s1
InChIKey 
LMJVXGOFWKVXAW-OXOINMOOSA-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
PF01966

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_00998.

PDB 4

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)