Binder profile

6DB

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

Bound to: PA1201 — transcriptional regulator

Via homolog PDB 5vvi UniProt P0A4T4 C9H18N4O4
Mol. weight 246.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6DB
PDB
5vvi
UniProt (similar protein)
P0A4T4
Target protein
PA1201

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 246.27 Da
LogP (Crippen) -1.23
H-bond donors 6
H-bond acceptors 4
TPSA 148.53 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 17
Fraction sp³ C 0.67
Formula C9H18N4O4

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 246.3
  • LogP ≤ 5 -1.23
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 148.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](C)C(=O)O
InChI 
InChI=1S/C9H18N4O4/c1-5(7(14)15)13-6(8(16)17)3-2-4-12-9(10)11/h5-6,13H,2-4H2,1H3,(H,14,15)(H,16,17)(H4,10,11,12)/t5-,6+/m1/s1
InChIKey 
IMXSCCDUAFEIOE-RITPCOANSA-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
PF03466

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA1201.

PDB 5

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)