Ligand profile

EM9

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

Bound to: KP13_03600 — putative oxidoreductase

Via homolog PDB 6dtp UniProt P14061 Formula C₃₄H₅₄ClNO₃
Mol. weight 560.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EM9
PDB
6dtp
UniProt (similar protein)
P14061
Target protein
KP13_03600

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 560.26 Da
LogP (Crippen) 8.21
H-bond donors 2
H-bond acceptors 3
TPSA 60.77 Ų
Rotatable bonds 14
Aromatic rings 1 / 4
Heavy atoms 39
Fraction sp³ C 0.79
Formula C₃₄H₅₄ClNO₃

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 60.8
  • −1 ≤ LogP ≤ 5 8.21
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 560.3
  • LogP ≤ 5 8.21
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 60.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCN(C)C(=O)CCCCCCCCCC[C@@H]1Cc2cc(ccc2[C@@H]3[C@@H]1[C@@H]4C[C@H]([C@@H]([C@]4(CC3)C)O)Cl)O
InChI 
InChI=1S/C34H54ClNO3/c1-4-5-20-36(3)31(38)15-13-11-9-7-6-8-10-12-14-24-21-25-22-26(37)16-17-27(25)28-18-19-34(2)29(32(24)28)23-30(35)33(34)39/h16-17,22,24,28-30,32-33,37,39H,4-15,18-21,23H2,1-3H3/t24-,28-,29+,30-,32-,33+,34+/m1/s1
InChIKey 
FQJIZXBCOKNLMR-FTAPQOLWSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00106

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_03600.

PDB 12

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

Ligand PDB entry

ChEMBL 100

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)