Validator^DB
Database of validation results for ligands and non-standard residues in the Protein Data Bank.

Molecules Examples of molecules which exhibit errors either very commonly, or very rarely throughout the PDB.

CLA

Incomplete structure and chirality errors on carbon
Chlorophyll a (CLA) is an important green pigment used in oxygenic photosynthesis. In contrast to its paramount importance, it is structurally one of the worst determined ligands in the PDB. More than half of the CLA molecules found in the PDB are incomplete, in general missing the entire hydrocarbon tail. A fifth of the molecules which are complete exhibit at least one chirality error on a carbon atom (especially C8). Overall, only 20% of CLA molecules are complete and correct.

DMU

Incomplete structure and chirality errors on carbon
n-Dodecyl-β-D-Maltoside (DMU) is a detergent used for the solubilization of membrane proteins to preserve their activity. Almost 40% of DMU molecules in the PDB are incomplete, missing rings or the hydrocarbon tail. Over a third of the structurally complete molecules exhibit multiple chirality issues.

NAP

Missing rings
The nicotinamide-adenine-dinucleotide phosphate (NAP) is an important cofactor in anabolic reactions. Approximately 8% of NAP molecules are incomplete, missing ring atoms. In the majority of cases, entire parts of the molecule are missing, rather than just a few atoms.

MLT

Chirality errors on carbon
D-malate (MLT) is the metabolic product of the naturally occurring L-malate (LMT). All the MLT molecules in the PDB are complete. However more than 40% of them exhibit wrong chirality on the C2 carbon, indicating that they are, in fact, incorrectly annotated LMTs.

ATP

Chirality errors on phosphorus
Adenosine triphosphate (ATP) is a coenzyme used for transporting chemical energy within cells for metabolism. Perhaps due to the fact that it is heavily studied, just a fraction of the ATP molecules in the PDB have incomplete structure.

HEM

Low error rate
This example illustrates a representative well-determined ligand, as almost all protoporphyrin ix molecules containing Fe (HEM) are structurally complete. All reported chirality errors lie on the planar Fe atom, most likely a result of slightly different puckering of the heme plane, and not a real chirality error.

FAD

Low error rate
Another example of a structurally well-determined ligand is the redox cofactor FAD (flavin-adenine dinucleotide). Again, almost all the FAD molecules in the PDB are structurally complete. Less than 3% of the validated FAD molecules exhibit chirality errors on carbon atoms.