Binder profile

ZINC168710640

Virtual-screening candidate from ZINC.

Bound to: PA3700 — lysine--tRNA ligase

Via homolog UniProt Q9RHV9 C15H22N8O8S

Tanimoto 0.81

Mol. weight 474.46 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: ZINC168710640
UniProt (similar protein): Q9RHV9
Tanimoto: 0.809
Target protein: PA3700

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 474.46 Da

LogP (Crippen) -4.00

H-bond donors 6

H-bond acceptors 14

TPSA 260.89 Å²

Rotatable bonds 9

Aromatic rings 2 / 3

Heavy atoms 32

Fraction sp³ C 0.53

Formula C15H22N8O8S

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 Å² and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

Lipinski's Rule of Five Fail 2 violations

MW ≤ 500 Da 474.5
LogP ≤ 5 -4.00
H-bond donors ≤ 5 6
H-bond acceptors ≤ 10 14

Veber's rules Fail

Rotatable bonds ≤ 10 9
TPSA ≤ 140 Å² 260.9

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

NC(=O)CC[C@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]1O

InChI

InChI=1S/C15H22N8O8S/c16-6(1-2-8(17)24)14(27)22-32(28,29)30-3-7-10(25)11(26)15(31-7)23-5-21-9-12(18)19-4-20-13(9)23/h4-7,10-11,15,25-26H,1-3,16H2,(H2,17,24)(H,22,27)(H2,18,19,20)/t6-,7+,10-,11-,15+/m0/s1

InChIKey

KXWKSWRGZLZHEF-HOHHYEBKSA-N

Provenance

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

Method: LigQ nearest_k
Query: KAA
Homolog: Q9RHV9

External resources

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

ZINC ZINC15 ZINC168710640 →
ZINC ZINC20 ZINC168710640 →
UniProt UniProt Q9RHV9 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “ZINC168710640”) →

Other binders for this protein

Quick navigation to other ligands bound to PA3700.

PDB 17

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

Ligand PDB entry

ChEMBL 2

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)