Binder profile

RIP

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

Bound to: PA1946 — ribose ABC transporter substrate-binding protein

Via homolog PDB 4zjp UniProt A6VKT0 C5H10O5
Mol. weight 150.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RIP
PDB
4zjp
UniProt (similar protein)
A6VKT0
Target protein
PA1946

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 150.13 Da
LogP (Crippen) -2.58
H-bond donors 4
H-bond acceptors 5
TPSA 90.15 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 10
Fraction sp³ C 1.00
Formula C5H10O5

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 150.1
  • LogP ≤ 5 -2.58
  • 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 
C1[C@H]([C@H]([C@H]([C@@H](O1)O)O)O)O
InChI 
InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3-,4-,5-/m1/s1
InChIKey 
SRBFZHDQGSBBOR-TXICZTDVSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF13407

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA1946.

PDB 1

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

Ligand PDB entry

ZINC 25

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

Compound Similarity (Tanimoto)