ARIEL — Help & Field Reference
This page describes every field in ARIEL. Each record is organized across different tables. A blank field indicates that the information was not reported in the source; blank values are never estimated.
Complex Table & Ligand Information
Structure and ligand identifiers shown at the top of each RNA–ligand complex entry.
| Field | Description |
|---|---|
| PDB ID/Extended PDB ID | PDB accession code of the structure (4-character or Extended PDB format). |
| Structure Method | Experimental method used to determine the structure: X-ray crystallography, cryo-EM, or NMR. |
| Resolution | Structural resolution in ångström (Å); blank for NMR structures. |
| Structure Title | Title of the PDB structure. |
| CCD ligand ID | PDB Chemical Component Dictionary (CCD) code of the bound ligand; links to the Ligand table. |
| Ligand Name | Chemical name of the ligand. |
| Ligand Auth Chain | Author chain identifier of the representative ligand copy. |
| Ligand Res Num | Residue number of the representative ligand copy. |
Ligand–RNA Binding Affinity & Assay Conditions
Experimental binding data and assay metadata reported in the literature.
| Field | Description |
|---|---|
| Affinity Type | Kd, Kd-macroscopic, Kd-apparent, or Kd-cooperative.
|
| Affinity Data | Dissociation constant (Kd) as reported in the source publication, with the original unit (nM, µM, or mM). |
| Affinity Data (M) | The reported Kd converted to molar units for comparison across entries. |
| pKd | Negative base-10 logarithm of Kd in molar units, −log10(Kd M); higher values indicate tighter binding. Colored badges use a red–yellow–green scale (weaker to stronger; see scale above). |
| Affinity Method | Experimental technique used to measure Kd (ITC, SPR, MST, NMR, or fluorescence). |
| Stoichiometry | Binding stoichiometry, e.g. 1(RNA):1(Ligand) or 1(RNA):2(Ligand). |
| Temperature | Assay temperature as reported in the source paper, in degrees Celsius (°C). The equivalent kelvin (K) is always recorded and shown alongside it on the entry detail page. |
| pH | pH of the binding assay; blank if not reported. |
| Buffer | Buffer composition or additional experimental conditions, recorded as free text. |
| Mg²⁺ (mM) | Magnesium ion concentration in the assay buffer, in millimolar. |
| ΔG (Experimental) | Binding free energy as reported in the source paper. Recorded only when measured experimentally; never back-calculated from Kd. |
| Kd Reference DOI | DOI of the publication reporting the Kd, when different from the structure paper. Same as Primary Reference if the Kd value is reported in the primary reference paper. |
| Kd Source Location | Location of the Kd within the source paper (table, figure, or text). |
| Multiple Kd Values | Other reported Kd values for the same RNA–ligand system (e.g. alternate buffer, metal ion, or binding site). Shown when curated in the dataset; blank if none or not applicable. |
RNA Sequence, Classification & Pocket Details
RNA target sequence, functional classification, and ligand-binding pocket composition.
| Field | Description |
|---|---|
| RNA Sequence | Sequence of the interacting RNA chain(s), written 5′→3′, with the corresponding interacting chain name. Multiple chains are shown separately. |
| Interacting RNA Chains | Author chain identifier(s) of the interacting RNA chains that form the binding pocket. |
| RNA Class | Functional class of the RNA: riboswitch, aptamer, ribozyme, rRNA, tRNA, mRNA element, viral, synthetic duplex, G-quadruplex, or other. |
| RNA Subclass | More specific classification where applicable (e.g. fluoride riboswitch, CAG-repeat). |
| Pocket Residues | RNA residues within 5 Å of the ligand, defining the binding pocket (see Methods). |
| Count of A | Number of adenine residues in the binding pocket. |
| Count of G | Number of guanine residues in the binding pocket. |
| Count of C | Number of cytosine residues in the binding pocket. |
| Count of U | Number of uracil residues in the binding pocket. |
| Modified Residues | Whether the RNA contains modified or non-standard nucleotides (yes/no). |
| Modified Residue List | List of modified residues present, if any. |
| Protein Contact | Whether the ligand also contacts a protein chain (yes/no). When yes, contacting residues can be viewed in a popover list. |
| Alt Copies | Additional crystallographic copies of the ligand within the same structure that were consolidated into this entry (ligand residue name, ligand chain, residue number, and interacting RNA chain(s)). |
Provenance
| Field | Description |
|---|---|
| Primary Reference | DOI of the publication describing the structure. |
| Related PDBs | Other PDB entries representing the same RNA–ligand pair in a separate deposition (accession codes only). |
| Remarks | Additional curator remarks about the entry. |
Ligand Table
Physicochemical descriptors and identifiers for each small-molecule ligand.
| Field | Description |
|---|---|
| Ligand Name | Common or chemical name of the ligand. |
| Molecular Weight | Molecular weight in daltons; blank for monoatomic ions. |
| SMILES | Canonical SMILES string of the ligand (from the CCD); blank for monoatomic ions. |
| InChIKey | Standard InChIKey identifier of the ligand. |
| PubChem CID | PubChem Compound identifier (assigned by cross-reference). |
| LogP (ALOGP) | OpenEye ALOGP lipophilicity computed from RCSB canonical SMILES (stored in the logP column). |
| Charge | Net formal charge of the ligand, expressed as positive, negative, or neutral. |
| QED | Quantitative Estimate of Drug-likeness (0–1). |
| Aromatic Rings | Number of aromatic rings in the ligand. |
| HBD | Number of hydrogen-bond donor groups in the ligand (see Methods). |
| HBA | Number of hydrogen-bond acceptor groups in the ligand (see Methods). |
Methods & Definitions
Binding pocket
The binding pocket is defined as the set of RNA residues having any heavy atom within 5 Å of any heavy atom of the ligand, computed directly from the structure. Each residue is counted once, regardless of how many of its atoms are within range. The fields Count of A, Count of G, Count of C, and Count of U give the base composition of the pocket. For mixed RNA–protein interfaces, both RNA and amino acid residues that are part of the binding pocket are counted.
Hydrogen-bond donors and acceptors
HBD and HBA are derived from the ligand's CCD definition using atom types and connectivity: nitrogen, oxygen, and sulfur atoms are counted as acceptors, and N–H, O–H, and S–H groups as donors. These values represent the ligand's intrinsic potential donors and acceptors, not the hydrogen bonds actually formed with the RNA.
Charge
The net formal charge of the ligand, obtained by summing the per-atom formal charges given in the CCD definition.
LogP (ALOGP)
OpenEye ALOGP lipophilicity computed from RCSB canonical SMILES via compute_qed_from_rcsb.py and stored in the logP column.
QED
QED drug-likeness score (0–1) from the silicos-it implementation using weighted mean property vectors (Bickerton et al., 2012). Computed alongside ALOGP from RCSB SMILES. Reference: silicos-it/qed.
Modified residues
A residue in an RNA chain is flagged as modified if it is a residue other than A, U, G, or C. This check is applied only to RNA polymer residues.
Protein contact
Recorded as “yes” when one or more amino acid residues lie close to the ligand, identifying entries in which the ligand is not bound to RNA alone.
Affinity standardization
The reported dissociation constant (Kd with its original unit) is converted to molar units (M) and expressed as pKd = −log10(Kd M) for uniform comparison across entries.
Representative selection
Across depositions: when several PDB entries represent the same RNA–ligand pair, the highest-resolution structure is chosen (then occupancy nearest 1, then lower pocket B-factor) as the primary record, and the other PDBs are listed in Related PDBs.
Within a structure: when one PDB contains several copies of the ligand, a single representative copy is kept (occupancy nearest 1, then lower pocket B-factor), and the dropped copies are recorded in Alt Copies.
Related PDBs versus Alt Copies
Related PDBs lists other PDB depositions of the same complex (between separate structures). Alt Copies lists other copies of the ligand within the same structure. The two are distinct.
RNA class assignment
Each entry is assigned to one of 11 RNA structural classes based on PDB entry titles and manual literature curation: Riboswitch — gene-regulatory RNAs binding small molecules to control transcription or translation; Aptamer — in vitro selected RNAs including fluorogenic and ligand-binding aptamers; rRNA (A-site model) — short oligonucleotides mimicking the 16S rRNA decoding A-site; snRNA / splice site — pre-mRNA splicing elements; Ribosome (full) — complete 70S or isolated ribosomal subunit structures; Repeat / G-quadruplex RNA — disease-associated repeat and G-quadruplex RNAs; Viral RNA — HIV-1 TAR, frameshift site, and influenza RNA; IRES — internal ribosome entry site elements; Ribozyme — catalytic RNAs; Group II intron; and RNA duplex / other. Note that rRNA (A-site model) and Ribosome are intentionally kept separate as short oligonucleotide models and intact ribosomal particles represent fundamentally different structural contexts for ligand binding.
Conventions
A blank field means the value was not reported and has not been estimated. Ionic cognate ligands, such as fluoride and Mn²⁺ in metal-sensing riboswitches, are retained; their molecular descriptor fields (SMILES, MW, HBD, HBA, num_rings, LogP, QED, and Charge) are left blank.