Ligand profile

ZINC4096578

Virtual-screening candidate from ZINC.

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

Via homolog UniProt P65870 Formula C₉H₁₃N₅O₄
Tanimoto 0.51
Mol. weight 255.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4096578
UniProt (similar protein)
P65870
Tanimoto
0.510
Target protein
KP13_02393

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 255.23 Da
LogP (Crippen) -2.44
H-bond donors 6
H-bond acceptors 8
TPSA 156.85 Ų
Rotatable bonds 3
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.44
Formula C₉H₁₃N₅O₄

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 156.8
  • −1 ≤ LogP ≤ 5 -2.44
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 255.2
  • LogP ≤ 5 -2.44
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 156.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(c(=O)[nH]1)N=C([C@H](O)[C@H](O)CO)CN2
InChI 
InChI=1S/C9H13N5O4/c10-9-13-7-5(8(18)14-9)12-3(1-11-7)6(17)4(16)2-15/h4,6,15-17H,1-2H2,(H4,10,11,13,14,18)/t4-,6+/m1/s1
InChIKey 
YQIFAMYNGGOTFB-XINAWCOVSA-N

Provenance

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

Method
LigQ sequence
Query
ZSP
Homolog
P65870

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)