Ligand profile

2K8

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

Bound to: KP13_02393 — 6-carboxy-5,6,7,8-tetrahydropterin synthase

Via homolog PDB 4ntm UniProt P65870 Formula C₇H₉N₅O₃
Mol. weight 211.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2K8
PDB
4ntm
UniProt (similar protein)
P65870
Target protein
KP13_02393

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 211.18 Da
LogP (Crippen) -1.36
H-bond donors 5
H-bond acceptors 6
TPSA 133.13 Ų
Rotatable bonds 1
Aromatic rings 1 / 2
Heavy atoms 15
Fraction sp³ C 0.29
Formula C₇H₉N₅O₃

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 133.1
  • −1 ≤ LogP ≤ 5 -1.36
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 211.2
  • LogP ≤ 5 -1.36
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 133.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H](NC2=C(N1)N=C(NC2=O)N)C(=O)O
InChI 
InChI=1S/C7H9N5O3/c8-7-11-4-3(5(13)12-7)10-2(1-9-4)6(14)15/h2,10H,1H2,(H,14,15)(H4,8,9,11,12,13)/t2-/m1/s1
InChIKey 
QSIYONWVWDSRRO-UWTATZPHSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF01242

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_02393.

PDB 2

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

Ligand PDB entry

ZINC 34

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

Compound Similarity (Tanimoto)