Ligand profile

CH5

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

Bound to: KP13_00647 — sn-glycerol-3-phosphate-binding periplasmic protein ugpB

Via homolog PDB 6r1b UniProt P71619 Formula C₈H₂₁NO₆P⁺
Mol. weight 258.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CH5
PDB
6r1b
UniProt (similar protein)
P71619
Target protein
KP13_00647

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 258.23 Da
LogP (Crippen) -0.82
H-bond donors 3
H-bond acceptors 5
TPSA 96.22 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 1.00
Formula C₈H₂₁NO₆P⁺

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 96.2
  • −1 ≤ LogP ≤ 5 -0.82
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 258.2
  • LogP ≤ 5 -0.82
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 96.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[N+](C)(C)CCO[P@](=O)(O)OC[C@@H](CO)O
InChI 
InChI=1S/C8H20NO6P/c1-9(2,3)4-5-14-16(12,13)15-7-8(11)6-10/h8,10-11H,4-7H2,1-3H3/p+1/t8-/m1/s1
InChIKey 
SUHOQUVVVLNYQR-MRVPVSSYSA-O

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
PF01547

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_00647.

PDB 9

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)