Ligand profile

SP1

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

Bound to: KP13_05031 — Fumarate nitrate reduction regulatory protein

Via homolog PDB 4r8h UniProt P0ACJ8 Formula C₁₀H₁₂N₅O₅PS
Mol. weight 345.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SP1
PDB
4r8h
UniProt (similar protein)
P0ACJ8
Target protein
KP13_05031

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 345.28 Da
LogP (Crippen) -0.70
H-bond donors 3
H-bond acceptors 10
TPSA 137.77 Ų
Rotatable bonds 1
Aromatic rings 2 / 4
Heavy atoms 22
Fraction sp³ C 0.50
Formula C₁₀H₁₂N₅O₅PS

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 137.8
  • −1 ≤ LogP ≤ 5 -0.70
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 345.3
  • LogP ≤ 5 -0.70
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 10
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 137.8
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]4[C@H](O3)CO[P@](=S)(O4)O)O)N
InChI 
InChI=1S/C10H12N5O5PS/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7-4(19-10)1-18-21(17,22)20-7/h2-4,6-7,10,16H,1H2,(H,17,22)(H2,11,12,13)/t4-,6-,7-,10-,21+/m1/s1
InChIKey 
SMPNJFHAPJOHPP-LHKKBNDGSA-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
PF00027' 'PF13545

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_05031.

PDB 5

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)