Binder profile

00A

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: PA2893 — long-chain-acyl-CoA synthetase

Via homolog PDB 3cw8 UniProt Q8GN86 C17H17ClN5O8P
Mol. weight 485.78 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
00A
PDB
3cw8
UniProt (similar protein)
Q8GN86
Target protein
PA2893

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 485.78 Da
LogP (Crippen) 0.66
H-bond donors 4
H-bond acceptors 12
TPSA 192.14 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 32
Fraction sp³ C 0.29
Formula C17H17ClN5O8P

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 1 violation
  • MW ≤ 500 Da 485.8
  • LogP ≤ 5 0.66
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 192.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C(=O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)Cl
InChI 
InChI=1S/C17H17ClN5O8P/c18-9-3-1-8(2-4-9)17(26)31-32(27,28)29-5-10-12(24)13(25)16(30-10)23-7-22-11-14(19)20-6-21-15(11)23/h1-4,6-7,10,12-13,16,24-25H,5H2,(H,27,28)(H2,19,20,21)/t10-,12-,13-,16-/m1/s1
InChIKey 
RVDNKWBGRIIRML-XNIJJKJLSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00501

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA2893.

PDB 11

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)