Ligand profile

MIY

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

Bound to: KP13_03630 — Acriflavine resistance protein B

Via homolog PDB 2drd UniProt P31224 Formula C₂₃H₂₇N₃O₇
Mol. weight 457.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MIY
PDB
2drd
UniProt (similar protein)
P31224
Target protein
KP13_03630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 457.48 Da
LogP (Crippen) 0.19
H-bond donors 5
H-bond acceptors 9
TPSA 164.63 Ų
Rotatable bonds 3
Aromatic rings 1 / 4
Heavy atoms 33
Fraction sp³ C 0.43
Formula C₂₃H₂₇N₃O₇

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 164.6
  • −1 ≤ LogP ≤ 5 0.19
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 457.5
  • LogP ≤ 5 0.19
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 164.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C)c1ccc(c2c1C[C@H]3C[C@H]4[C@@H](C(=C(C(=O)[C@]4(C(=C3C2=O)O)O)C(=O)N)O)N(C)C)O
InChI 
InChI=1S/C23H27N3O7/c1-25(2)12-5-6-13(27)15-10(12)7-9-8-11-17(26(3)4)19(29)16(22(24)32)21(31)23(11,33)20(30)14(9)18(15)28/h5-6,9,11,17,27,29-30,33H,7-8H2,1-4H3,(H2,24,32)/t9-,11-,17-,23-/m0/s1
InChIKey 
DYKFCLLONBREIL-KVUCHLLUSA-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)