Ligand profile

RM4

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

Bound to: KP13_03396 — 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase

Via homolog PDB 7do7 UniProt C1DMX5 Formula C₆H₁₂O₅
Mol. weight 164.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RM4
PDB
7do7
UniProt (similar protein)
C1DMX5
Target protein
KP13_03396

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 164.16 Da
LogP (Crippen) -2.19
H-bond donors 4
H-bond acceptors 5
TPSA 90.15 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 11
Fraction sp³ C 1.00
Formula C₆H₁₂O₅

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 90.2
  • −1 ≤ LogP ≤ 5 -2.19
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 164.2
  • LogP ≤ 5 -2.19
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 90.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O)O)O)O
InChI 
InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6-/m0/s1
InChIKey 
SHZGCJCMOBCMKK-YJRYQGEOSA-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
PF13561

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_03396.

PDB 6

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)