Binder profile

EM9

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

Bound to: PA1330 — short-chain dehydrogenase

Via homolog PDB 6dtp UniProt P14061 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
PA1330

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.

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 TPW 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 binders for this protein

Quick navigation to other ligands bound to PA1330.

PDB 15

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)