Ligand profile

CZJ

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

Bound to: KP13_00007 — Ribose import ATP-binding protein rbsA

Via homolog PDB 6b8b UniProt P0A9V1 Formula C₃₀H₃₈N₂O₁₀
Mol. weight 586.64 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CZJ
PDB
6b8b
UniProt (similar protein)
P0A9V1
Target protein
KP13_00007

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 586.64 Da
LogP (Crippen) 3.32
H-bond donors 4
H-bond acceptors 10
TPSA 179.78 Ų
Rotatable bonds 6
Aromatic rings 2 / 7
Heavy atoms 42
Fraction sp³ C 0.63
Formula C₃₀H₃₈N₂O₁₀

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 179.8
  • −1 ≤ LogP ≤ 5 3.32
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 586.6
  • LogP ≤ 5 3.32
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 179.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)C34CC5CC(C3)CC(C5)C4)O[C@H]6[C@@H]([C@@H]([C@H](C(O6)(C)C)OC)OC(=O)N)O
InChI 
InChI=1S/C30H38N2O10/c1-13-18(39-26-21(34)23(41-28(31)37)24(38-4)29(2,3)42-26)6-5-17-20(33)19(25(35)40-22(13)17)32-27(36)30-10-14-7-15(11-30)9-16(8-14)12-30/h5-6,14-16,21,23-24,26,33-34H,7-12H2,1-4H3,(H2,31,37)(H,32,36)/t14?,15?,16?,21-,23+,24-,26-,30?/m1/s1
InChIKey 
SFCPIJFPMNEBLW-YSDKWAIISA-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
PF00005

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_00007.

PDB 12

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)