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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
4yuv S4M Spermidine synthase, putative

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4yuv S4MSpermidine synthase, putative / 1.148
4yv1 S4MSpermidine synthase, putative / 1.009
4yuz S4MSpermidine synthase, putative / 0.974
4yv2 S4MSpermidine synthase, putative / 0.945
4yv0 S4MSpermidine synthase, putative / 0.910
2pt6 S4MSpermidine synthase / 0.816
2o07 MTASpermidine synthase 2.5.1.16 0.799
1jq3 AATPolyamine aminopropyltransferase / 0.760
3bwc SAMSpermidine synthase, putative / 0.737
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.731
2o06 MTASpermidine synthase 2.5.1.16 0.724
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.723
3rw9 DSHSpermidine synthase 2.5.1.16 0.719
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.707
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.701
1ek5 NADUDP-glucose 4-epimerase / 0.689
1y9d FADPyruvate oxidase 1.2.3.3 0.686
4nec SAHPutative SAM-dependent methyltransferase / 0.686
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.684
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.683
1g1a NADdTDP-glucose 4,6-dehydratase / 0.682
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.682
3ko8 NADNAD-dependent epimerase/dehydratase / 0.681
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.681
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.680
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.680
2g1p SAHDNA adenine methylase 2.1.1.72 0.679
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.676
4yac NAIC alpha-dehydrogenase / 0.674
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.670
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.669
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.667
1boo SAHModification methylase PvuII 2.1.1.113 0.666
1wy7 SAHUncharacterized protein / 0.666
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.664
3fpf MTAUncharacterized protein / 0.664
2c7q SAHModification methylase HhaI 2.1.1.37 0.663
3ou6 SAMSAM-dependent methyltransferase / 0.663
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.661
4hh4 SAHCcbJ / 0.659
2pan FADGlyoxylate carboligase 4.1.1.47 0.656
5jla NADPutative short-chain dehydrogenase/reductase / 0.655
3s55 NADPutative short-chain dehydrogenase/reductase / 0.654
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.654
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.653
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.652
2z6u SAHModification methylase HhaI 2.1.1.37 0.652
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.652
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.651
2uyh SAHModification methylase HhaI 2.1.1.37 0.651
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.650
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.650
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.650