Binder profile

3YI

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

Bound to: PA3676 — resistance-nodulation-cell division (RND) efflux transporter

Via homolog PDB 6zoh UniProt P31224 C38H47NO13
Mol. weight 725.79 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
3YI
PDB
6zoh
UniProt (similar protein)
P31224
Target protein
PA3676

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 725.79 Da
LogP (Crippen) 4.57
H-bond donors 6
H-bond acceptors 13
TPSA 218.38 Ų
Rotatable bonds 3
Aromatic rings 2 / 5
Heavy atoms 52
Fraction sp³ C 0.47
Formula C38H47NO13

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 3 violations
  • MW ≤ 500 Da 725.8
  • LogP ≤ 5 4.57
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 218.4
PAINS Alert

Matches PAINS filter: keto_naphthol_A(2). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](/C=C/C=C(\C(=O)Nc(c2O)c(c3O)C=O)/C)C)O)C)O)C)OC(=O)C)C)OC)C)O
InChI 
InChI=1S/C38H47NO13/c1-16-11-10-12-17(2)37(48)39-28-23(15-40)32(45)25-26(33(28)46)31(44)21(6)35-27(25)36(47)38(8,52-35)50-14-13-24(49-9)18(3)34(51-22(7)41)20(5)30(43)19(4)29(16)42/h10-16,18-20,24,29-30,34,42-46H,1-9H3,(H,39,48)/b11-10+,14-13+,17-12-/t16-,18+,19+,20+,24-,29-,30+,34+,38-/m0/s1
InChIKey 
BBNQHOMJRFAQBN-UPZFVJMDSA-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
PF00873

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3676.

PDB 32

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

Ligand PDB entry

ChEMBL 53

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)