Binder profile

ZINC5080460

Virtual-screening candidate from ZINC.

Bound to: PA3947 — DNA-binding response regulator RocR

Via homolog UniProt Q9HX69 C13H17N5O5
Tanimoto 0.66
Mol. weight 323.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5080460
UniProt (similar protein)
Q9HX69
Tanimoto
0.656
Target protein
PA3947

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 323.31 Da
LogP (Crippen) -0.89
H-bond donors 3
H-bond acceptors 9
TPSA 137.51 Ų
Rotatable bonds 1
Aromatic rings 2 / 4
Heavy atoms 23
Fraction sp³ C 0.62
Formula C13H17N5O5

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 323.3
  • LogP ≤ 5 -0.89
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 137.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1(C)OC[C@@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@@H](O)[C@@H]2O1
InChI 
InChI=1S/C13H17N5O5/c1-13(2)21-3-5-8(23-13)7(19)11(22-5)18-4-15-6-9(18)16-12(14)17-10(6)20/h4-5,7-8,11,19H,3H2,1-2H3,(H3,14,16,17,20)/t5-,7-,8+,11+/m0/s1
InChIKey 
VDVHAPVSQCJZHA-WOIOKPISSA-N

Provenance

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

Method
LigQ sequence
Query
C2E
Homolog
Q9HX69

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3947.

PDB 1

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

Ligand PDB entry

ChEMBL 3

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

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

Compound Similarity (Tanimoto)