Binder profile

ZINC3869969

Virtual-screening candidate from ZINC.

Bound to: PA3551 — bifunctional mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase

Via homolog UniProt Q9X0C3 C10H13N5O5
Tanimoto 0.67
Mol. weight 283.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3869969
UniProt (similar protein)
Q9X0C3
Tanimoto
0.672
Target protein
PA3551

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 283.24 Da
LogP (Crippen) -2.69
H-bond donors 5
H-bond acceptors 9
TPSA 159.51 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.50
Formula C10H13N5O5

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 283.2
  • LogP ≤ 5 -2.69
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 159.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c(=O)[nH]1
InChI 
InChI=1S/C10H13N5O5/c11-10-13-7-4(8(19)14-10)12-2-15(7)9-6(18)5(17)3(1-16)20-9/h2-3,5-6,9,16-18H,1H2,(H3,11,13,14,19)/t3-,5+,6-,9-/m0/s1
InChIKey 
NYHBQMYGNKIUIF-HFXAWCPLSA-N

Provenance

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

Method
LigQ nearest_k
Query
GDD
Homolog
Q9X0C3

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA3551.

PDB 1

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)