Ligand profile

3YI

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

Bound to: KP13_03630 — Acriflavine resistance protein B

Via homolog PDB 6zoh UniProt P31224 Formula 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
KP13_03630

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.

  • TPSA ≤ 90 Ų 218.4
  • −1 ≤ LogP ≤ 5 4.57
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 Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00873

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to KP13_03630.

PDB 33

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)