SMARTFlexDB

SMARTFlexDB

RNA · apo–holo · structural comparison

Explore structural differences between ligand-free and ligand-bound RNA pockets

SMARTFlexDB is a curated database of matched ligand-free (apo) and ligand-bound (holo) RNA structures. The current release contains binding pockets from holo structures, compared with apo structures in pocket-level apo–holo comparisons ( apo–holo database entries), spanning PDB structures, small molecules and RNA functional classes.

Each record includes aligned 3D structures, a 2D secondary-structure comparison, an interpolated apo→holo morph, sequence alignments, pocket-level measurements, and ligand–RNA interaction data.

apo–holo entries

PDB structures

unique ligands

functional types

Browse the Database Run a Query

5SWE adenine riboswitch, apo end of the morph

Riboswitch ▶ play morph 5SWE · ADE apo–holo Adenine riboswitch converted in crystal by ligand mixing · rmsd

HIV TAR ▶ play morph 2L8H · L8H apo–holo HIV-1 TAR structural difference · vs apo · rmsd

Every pair includes Superposed apo and holo structures Interpolated apo–holo morph 2D secondary-structure diagrams Ligand–RNA contacts Local and global sequence identity

What an entry looks like

SMARTFlexDB matches a ligand-bound (holo) binding site to a ligand-free (apo) structure of the same RNA, superposes them over every binding-site chain at once, and measures what moved: global and pocket RMSD, each chain’s shift and the sequence identity. Open the entry to explore all bound ligands of the holo structure.

Open this entry

holo apo

RMSD (Å) Pocket RMSD (Å) Global identity (%)

See the full comparison

A structurally diverse, redundancy-reduced RNA dataset

SMARTFlexDB provides sequence-, structure-, and pocket-level cluster assignments to support redundancy-aware dataset splits. Each map shows the relevant sequence, RNA chain, or binding pocket colored by cluster. See Clustering for thresholds, definitions, and limitations.

Functional type (NAKB) · counts are binding pockets

Open the Clustering map → download cluster assignments (CSV)

each point = one binding pocket · color = redundancy cluster

SMARTFlexDB

Explore structural differences between ligand-free and ligand-bound RNA pockets

What an entry looks like

A structurally diverse, redundancy-reduced RNA dataset

Everything you can do

Database gallery

Query your own

Multi-ligand pocket groups

Clustering & redundancy

Statistics