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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3vtk ADP Thymidine kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3vtk ADPThymidine kinase / 0.988
1sxj ADPReplication factor C subunit 5 / 0.733
4jlo ADPAdenylate kinase / 0.724
4cf7 ADPAdenylate kinase / 0.720
4ike ADPAdenylate kinase / 0.718
4jld ADPAdenylate kinase / 0.709
4jl5 ADPAdenylate kinase / 0.705
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.689
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.688
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.687
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.687
4jl6 ADPAdenylate kinase / 0.680
2whx ADPGenome polyprotein 3.4.21.91 0.677
1xmv ADPProtein RecA / 0.676
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.676
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.670
2gm1 ADPKinesin-like protein KIF11 / 0.669
2fna ADPUncharacterized protein / 0.667
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.666
1zio AP5Adenylate kinase / 0.666
3l9h ADPKinesin-like protein KIF11 / 0.665
1w5s ADPORC1-type DNA replication protein 2 / 0.664
4hse ADPChaperone protein ClpB / 0.662
2zts ADPUncharacterized protein / 0.661
4b7b ADPKinesin-like protein KIF11 / 0.661
1v8k ANPKinesin-like protein KIF2C / 0.660
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.660
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.660
2ql6 ADPNicotinamide riboside kinase 1 / 0.659
4mkg AP5Adenylate kinase / 0.659
2dft ADPShikimate kinase 2.7.1.71 0.656
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.656
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.656
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.655
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
1n6m ADPProtein claret segregational / 0.655
2y65 ADPKinesin heavy chain / 0.655
1svl ADPLarge T antigen 3.6.4 0.654
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.653
4gp6 ADPMetallophosphoesterase / 0.653
3pcr GTPADP-ribosylation factor 6 / 0.652
5fm6 ADPRuvB-like helicase / 0.652
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.651
4g01 GDPRas-related protein RABF2b / 0.651
4pjj ADPUnconventional myosin-VI / 0.651
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.651
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.650
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650