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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
3w2w ATP CRISPR system Cmr subunit Cmr2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3w2w ATPCRISPR system Cmr subunit Cmr2 / 1.099
5i4n ATPTyrosine-protein kinase JAK2 / 0.759
4fvr ATPTyrosine-protein kinase JAK2 / 0.740
1cjv DADAdenylate cyclase type 2 / 0.729
1cjv DADAdenylate cyclase type 5 / 0.729
4dtp DGTDNA-directed DNA polymerase / 0.723
4m42 ATPDNA-directed DNA polymerase / 0.712
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.711
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.710
3t3f N5PDNA polymerase I, thermostable 2.7.7.7 0.709
4dtj TTPDNA-directed DNA polymerase / 0.709
3hav ATPAminoglycoside phosphotransferase / 0.707
4df4 0L3DNA polymerase I, thermostable 2.7.7.7 0.706
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.706
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.704
4h5d YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.704
3g6x DGTDNA polymerase iota 2.7.7.7 0.694
4khy TTPDNA-directed DNA polymerase / 0.694
3kmw ATPIntegrin-linked protein kinase 2.7.11.1 0.684
5erm 210Fusicoccadiene synthase 4.2.3.43 0.683
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.682
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.681
2idx ATPCob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial 2.5.1.17 0.681
4fjj TTPDNA-directed DNA polymerase / 0.679
4fjm DCPDNA-directed DNA polymerase / 0.678
3ahj TPPProbable phosphoketolase / 0.675
3qt6 2P0Mevalonate diphosphate decarboxylase / 0.675
4dwb 0M7Farnesyl pyrophosphate synthase / 0.675
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.674
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.674
4xj4 3ATCyclic GMP-AMP synthase / 0.674
1mdr APGMandelate racemase / 0.673
1r89 CTPCCA-adding enzyme 2.7.7.72 0.673
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.672
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.672
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.670
1yv5 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.668
1dtn APGMandelate racemase / 0.666
1pvg ANPDNA topoisomerase 2 5.99.1.3 0.666
2rgg GNPGTPase HRas / 0.666
1wc5 APCAdenylate cyclase / 0.665
4dtx TTPDNA-directed DNA polymerase / 0.665
4fjh DGTDNA-directed DNA polymerase / 0.665
4fjl DGTDNA-directed DNA polymerase / 0.664
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.661
2whx ADPGenome polyprotein 3.4.21.91 0.661
3hiy UTPUncharacterized protein / 0.661
1jsz NDMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 2.1.1.57 0.660
3l1c ADPProtein claret segregational / 0.660
4bzb DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.660
3lzj CTPDNA-directed DNA polymerase / 0.659
1n2e APCPantothenate synthetase 6.3.2.1 0.658
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.657
1mx0 ANPType 2 DNA topoisomerase 6 subunit B / 0.654
1q6n P90Tyrosine-protein phosphatase non-receptor type 1 3.1.3.48 0.654
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.654
4dem YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.653
4l2x YL2Farnesyl pyrophosphate synthase 2.5.1.10 0.652
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.651
1x09 IPEDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) 2.5.1.31 0.651
1q6p 213Tyrosine-protein phosphatase non-receptor type 1 3.1.3.48 0.650
4to4 DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.650
5ero 210Fusicoccadiene synthase 2.5.1.29 0.650