Ligand profile

EBO

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

Bound to: KP13_00570 — Cystathionine gamma-synthase

Via homolog PDB 6lgo UniProt Q5H1U9 Formula C₁₆H₂₄N₃O₈PS
Mol. weight 449.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EBO
PDB
6lgo
UniProt (similar protein)
Q5H1U9
Target protein
KP13_00570

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 449.42 Da
LogP (Crippen) 0.57
H-bond donors 6
H-bond acceptors 8
TPSA 203.63 Ų
Rotatable bonds 12
Aromatic rings 1 / 1
Heavy atoms 29
Fraction sp³ C 0.50
Formula C₁₆H₂₄N₃O₈PS

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 203.6
  • −1 ≤ LogP ≤ 5 0.57
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 449.4
  • LogP ≤ 5 0.57
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 203.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)CP(=O)(O)O)/C=N/[C@@H](CCSCC[C@@H](C(=O)O)N)C(=O)O)O
InChI 
InChI=1S/C16H24N3O8PS/c1-9-14(20)11(10(6-18-9)8-28(25,26)27)7-19-13(16(23)24)3-5-29-4-2-12(17)15(21)22/h6-7,12-13,20H,2-5,8,17H2,1H3,(H,21,22)(H,23,24)(H2,25,26,27)/b19-7+/t12-,13-/m0/s1
InChIKey 
QGHPUHOZHNBFHZ-VNBISDOUSA-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
PF01053

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_00570.

PDB 6

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

Ligand PDB entry

ChEMBL 2

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 25

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

Compound Similarity (Tanimoto)