Ligand profile

ZINC12428336

Virtual-screening candidate from ZINC.

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

Via homolog UniProt C6KTB6 Formula C₉H₁₁N₅O₄
Tanimoto 0.74
Mol. weight 253.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12428336
UniProt (similar protein)
C6KTB6
Tanimoto
0.738
Target protein
KP13_02393

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 253.22 Da
LogP (Crippen) -2.32
H-bond donors 5
H-bond acceptors 8
TPSA 158.24 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 18
Fraction sp³ C 0.33
Formula C₉H₁₁N₅O₄

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 158.2
  • −1 ≤ LogP ≤ 5 -2.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 253.2
  • LogP ≤ 5 -2.32
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 158.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2ncc([C@H](O)[C@H](O)CO)nc2c(=O)[nH]1
InChI 
InChI=1S/C9H11N5O4/c10-9-13-7-5(8(18)14-9)12-3(1-11-7)6(17)4(16)2-15/h1,4,6,15-17H,2H2,(H3,10,11,13,14,18)/t4-,6+/m1/s1
InChIKey 
BMQYVXCPAOLZOK-XINAWCOVSA-N

Provenance

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

Method
LigQ nearest_k
Query
BIO
Homolog
C6KTB6

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 3

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

Ligand PDB entry

ZINC 33

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

Compound Similarity (Tanimoto)