Ligand profile

BIO

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 1y13 UniProt C6KTB6 Formula C₉H₁₁N₅O₃
Mol. weight 237.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BIO
PDB
1y13
UniProt (similar protein)
C6KTB6
Target protein
KP13_02393

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 237.22 Da
LogP (Crippen) -1.29
H-bond donors 4
H-bond acceptors 7
TPSA 138.01 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 17
Fraction sp³ C 0.33
Formula C₉H₁₁N₅O₃

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 138.0
  • −1 ≤ LogP ≤ 5 -1.29
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 237.2
  • LogP ≤ 5 -1.29
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 138.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]([C@H](c1cnc2c(n1)C(=O)NC(=N2)N)O)O
InChI 
InChI=1S/C9H11N5O3/c1-3(15)6(16)4-2-11-7-5(12-4)8(17)14-9(10)13-7/h2-3,6,15-16H,1H3,(H3,10,11,13,14,17)/t3-,6-/m1/s1
InChIKey 
LHQIJBMDNUYRAM-AWFVSMACSA-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
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)