Ligand profile

D1S

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

Bound to: KP13_32123 — chaperone protein HtpG

Via homolog PDB 3q5j UniProt Q4Q4I6 Formula C₃₃H₅₀N₄O₈
Mol. weight 630.78 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
D1S
PDB
3q5j
UniProt (similar protein)
Q4Q4I6
Target protein
KP13_32123

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 630.78 Da
LogP (Crippen) 2.30
H-bond donors 4
H-bond acceptors 10
TPSA 169.52 Ų
Rotatable bonds 8
Aromatic rings 0 / 2
Heavy atoms 45
Fraction sp³ C 0.58
Formula C₃₃H₅₀N₄O₈

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 169.5
  • −1 ≤ LogP ≤ 5 2.30
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 630.8
  • LogP ≤ 5 2.30
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 169.5
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)NCCCN(C)C)/C)OC)OC(=O)N)\C)C)O)OC
InChI 
InChI=1S/C33H50N4O8/c1-19-15-23-28(35-13-10-14-37(5)6)25(38)18-24(30(23)40)36-32(41)20(2)11-9-12-26(43-7)31(45-33(34)42)22(4)17-21(3)29(39)27(16-19)44-8/h9,11-12,17-19,21,26-27,29,31,35,39H,10,13-16H2,1-8H3,(H2,34,42)(H,36,41)/b12-9-,20-11+,22-17+/t19-,21+,26+,27+,29-,31+/m1/s1
InChIKey 
UNPSMUMJWYZQHC-CYVBNFEDSA-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)