Binder profile

TDM

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

Bound to: PA3506 — hypothetical protein

Via homolog PDB 3e9y UniProt P17597 C14H22N4O8P2S
Mol. weight 468.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TDM
PDB
3e9y
UniProt (similar protein)
P17597
Target protein
PA3506

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 468.37 Da
LogP (Crippen) 2.51
H-bond donors 5
H-bond acceptors 10
TPSA 188.56 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 29
Fraction sp³ C 0.43
Formula C14H22N4O8P2S

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 468.4
  • LogP ≤ 5 2.51
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 188.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ncc(c(n1)N)CN\2C(=C(S/C2=C(\C)/O)CCO[P@@](=O)(O)OP(=O)(O)O)C
InChI 
InChI=1S/C14H22N4O8P2S/c1-8-12(4-5-25-28(23,24)26-27(20,21)22)29-14(9(2)19)18(8)7-11-6-16-10(3)17-13(11)15/h6,19H,4-5,7H2,1-3H3,(H,23,24)(H2,15,16,17)(H2,20,21,22)/b14-9+
InChIKey 
ZZLCKFKIIVXBQU-NTEUORMPSA-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
PF02775' 'PF02776

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3506.

PDB 13

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

Ligand PDB entry

ChEMBL 38

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

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)