Research :: pocketZebra :: Examples

1. Family of Protein kinases (catalytic subunit)
  • JobID b6896b1021cfa9 (link to the results page)
  • Download the Multiple sequence alignment
  • Download the PDB file 3K5V
  • Number of random shuffles: 10'000
Functionally important Subfamily-specific binding sites:
  • Primary functional site: POC0 and POC1 (ranks 1 and 3) bind STI (4-[(4-methylpiperazin-1-yl)methyl]-N-(4-methyl-3-{[4-(pyridin-3-yl)pyrimidin-2-yl]amino}phenyl)benzamide from 3K5V)
  • Secondary functional site 1: POC2 (rank 2) binds STJ (3-(6-{[4-(trifluoromethoxy)phenyl]amino}pyrimidin- 4-yl)benzamide from 3K5V)
  • Secondary functional site 2: POC7 (rank 4) binds A06 ((3S)-4-(5-chloro-1H-benzimidazol-2-yl)-3-(4-chlorophenyl)butanoic acid from 4A06)


2. Family of Dihydropteroate synthetases
  • JobID e95cec163c5c62 (link to the results page)
  • Download the Multiple sequence alignment
  • Download the PDB file 1AJZ
  • Number of random shuffles: 10'000
Functionally important Subfamily-specific binding sites:
  • Primary functional site: POC2 and POC4 (ranks 1 and 2) bind PH2 (2-amino-6-(hydroxymethyl)-7,8-dihydropteridin-4(3H)-one, from 1AJ0) and SAN (sulfanilamide, from 1AJ0)


3. Family of Aminoglycoside 3’-Phosphotransferases
  • JobID 64e25f75892eac (link to the results page)
  • Download the Multiple sequence alignment
  • Download the PDB file 4GKI
  • Number of random shuffles: 10'000
Functionally important Subfamily-specific binding sites:
  • Primary functional site: POC0 and POC4 (ranks 1 and 4) bind 0JN (1-tert-butyl-3-(naphthalen-1-ylmethyl)-1H- pyrazolo[3,4-d]pyrimidin-4-amine from 4GKI)
  • Secondary functional site: POC2 (rank 2) binds KAN (Kanamycin A from 4GKI)


4. Family of RNA polymerases (beta chain)
  • JobID 23cdcaf5d002ba (link to the results page, please be patient while ~20 MB download to your computer).
Functionally important Subfamily-specific binding sites:
  • Secondary functional site 1: POC178 (rank 3) binds RFP (Rifampicin, from 1YNN)
  • Secondary functional site 2: POC79 (rank8) binds NE6 (Myxopyronin, from 4A06)


Test set
Quantitative assessment and comparison of pocketZebra with previously published algorithms was performed on a set of proteins that were experimentally shown to possess at least two independent binding sites that can be classified by function as primary or secondary. Results of the evaluation have been discussed in

Suplatov D., Kirilin E., Arbatsky M., Takhaveev V., Švedas V. (2014) pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families. Nucl. Acids Res. 42(W1): W344-W349. DOI:dx.doi.org