Binder profile

ZINC32023359

Virtual-screening candidate from ZINC.

Bound to: PA5337 — DNA-directed RNA polymerase subunit omega

Via homolog UniProt P0A800 C11H16N5O11P3
Tanimoto 0.63
Mol. weight 487.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC32023359
UniProt (similar protein)
P0A800
Tanimoto
0.629
Target protein
PA5337

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 487.20 Da
LogP (Crippen) 0.16
H-bond donors 6
H-bond acceptors 11
TPSA 249.41 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 30
Fraction sp³ C 0.36
Formula C11H16N5O11P3

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 Fail 2 violations
  • MW ≤ 500 Da 487.2
  • LogP ≤ 5 0.16
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 249.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(ncn2[C@@H]2C=C[C@H](CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)C2)c(=O)[nH]1
InChI 
InChI=1S/C11H16N5O11P3/c12-11-14-9-8(10(17)15-11)13-5-16(9)7-2-1-6(3-7)4-25-29(21,22)27-30(23,24)26-28(18,19)20/h1-2,5-7H,3-4H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,12,14,15,17)/t6-,7+/m0/s1
InChIKey 
CQCAEOCIDCCJDQ-NKWVEPMBSA-N

Provenance

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

Method
LigQ nearest_k
Query
0O2
Homolog
P0A800

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA5337.

PDB 2

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)