Ligand profile

GDM

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

Bound to: KP13_32123 — chaperone protein HtpG

Via homolog PDB 4xdm UniProt P54651 Formula C₂₉H₄₀N₂O₉
Mol. weight 560.64 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
GDM
PDB
4xdm
UniProt (similar protein)
P54651
Target protein
KP13_32123

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 560.64 Da
LogP (Crippen) 2.41
H-bond donors 3
H-bond acceptors 9
TPSA 163.48 Ų
Rotatable bonds 4
Aromatic rings 0 / 2
Heavy atoms 40
Fraction sp³ C 0.52
Formula C₂₉H₄₀N₂O₉

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 163.5
  • −1 ≤ LogP ≤ 5 2.41
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 560.6
  • LogP ≤ 5 2.41
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 163.5
PAINS Alert

Matches PAINS filter: quinone_A(370). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1C[C@@H]([C@@H]([C@H](\C=C(\[C@@H]([C@H](\C=C/C=C(/C(=O)NC2=CC(=O)C(=C(C1)C2=O)OC)\C)OC)OC(=O)N)/C)C)O)OC
InChI 
InChI=1S/C29H40N2O9/c1-15-11-19-25(34)20(14-21(32)27(19)39-7)31-28(35)16(2)9-8-10-22(37-5)26(40-29(30)36)18(4)13-17(3)24(33)23(12-15)38-6/h8-10,13-15,17,22-24,26,33H,11-12H2,1-7H3,(H2,30,36)(H,31,35)/b10-8-,16-9+,18-13+/t15-,17+,22+,23+,24-,26+/m1/s1
InChIKey 
QTQAWLPCGQOSGP-KSRBKZBZSA-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
PF02518

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_32123.

PDB 27

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

Ligand PDB entry

ChEMBL 6

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)