Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
4yv2 S4M Spermidine synthase, putative

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4yv2 S4MSpermidine synthase, putative / 1.080
4yuz S4MSpermidine synthase, putative / 1.026
4yv1 S4MSpermidine synthase, putative / 0.974
4yuv S4MSpermidine synthase, putative / 0.945
4yv0 S4MSpermidine synthase, putative / 0.916
2pt6 S4MSpermidine synthase / 0.859
2o07 MTASpermidine synthase 2.5.1.16 0.802
2o06 MTASpermidine synthase 2.5.1.16 0.793
3bwc SAMSpermidine synthase, putative / 0.785
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.762
3rw9 DSHSpermidine synthase 2.5.1.16 0.758
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.739
3tsc NADUncharacterized protein / 0.732
5je4 SAHMethyl transferase / 0.729
2ibt NEAModification methylase TaqI 2.1.1.72 0.727
3ou6 SAMSAM-dependent methyltransferase / 0.727
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.724
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.724
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.723
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.723
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.723
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.722
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.722
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.718
1jq3 AATPolyamine aminopropyltransferase / 0.715
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.715
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.715
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.712
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.711
2rgh FADAlpha-Glycerophosphate Oxidase / 0.710
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.708
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.707
1orr NADCDP-paratose 2-epimerase / 0.706
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.706
3fpf MTAUncharacterized protein / 0.705
3cbg SAHO-methyltransferase / 0.703
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.702
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.700
3s55 NADPutative short-chain dehydrogenase/reductase / 0.699
1g1a NADdTDP-glucose 4,6-dehydratase / 0.698
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.697
1y9d FADPyruvate oxidase 1.2.3.3 0.696
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.696
3tos SAHCalS11 / 0.696
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.695
1boo SAHModification methylase PvuII 2.1.1.113 0.693
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.693
4tm3 FADKtzI / 0.693
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.693
2g1p SAHDNA adenine methylase 2.1.1.72 0.692
4kvz SAHPtnL protein / 0.692
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.691
2b69 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.691
2q7v FADThioredoxin reductase / 0.691
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.691
4rtk SAHDNA adenine methylase 2.1.1.72 0.691
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.690
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.690
3ldg SAHUncharacterized protein / 0.690
4tlz FADKtzI / 0.690
2hmv ADPKtr system potassium uptake protein A / 0.689
2bra FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.688
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.688
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.687
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.686
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.686
7mht SAHModification methylase HhaI 2.1.1.37 0.686
1f3l SAHProtein arginine N-methyltransferase 3 / 0.685
1g60 SAMModification methylase MboII 2.1.1.72 0.683
1nw5 SAMModification methylase RsrI 2.1.1.72 0.682
2ih5 NEAModification methylase TaqI 2.1.1.72 0.682
3sx2 NADUncharacterized protein / 0.682
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.682
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.680
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.680
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.679
4rtq SAHDNA adenine methylase 2.1.1.72 0.679
1nw6 SFGModification methylase RsrI 2.1.1.72 0.678
1yf3 SAHDNA adenine methylase / 0.678
2yxl SFG450aa long hypothetical fmu protein / 0.678
2i9k SAHModification methylase HhaI 2.1.1.37 0.677
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.676
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.676
3nyc FADFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.676
5je2 SAHMethyl transferase / 0.676
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.675
3cox FADCholesterol oxidase 1.1.3.6 0.675
1g38 NEAModification methylase TaqI 2.1.1.72 0.673
2ore SAHDNA adenine methylase 2.1.1.72 0.671
3go4 SAHUncharacterized protein / 0.670
4hb9 FADUncharacterized protein / 0.670
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.669
1y56 FAD382aa long hypothetical sarcosine oxidase / 0.669
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
2uyh SAHModification methylase HhaI 2.1.1.37 0.669
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.669
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.668
3he3 FADUDP-galactopyranose mutase / 0.668
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.668
3mht SAHModification methylase HhaI 2.1.1.37 0.667
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.667
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.666
3mj4 FADUDP-galactopyranose mutase / 0.666
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.665
1cbo FADCholesterol oxidase 1.1.3.6 0.665
1mxt FAECholesterol oxidase 1.1.3.6 0.665
1n1p FADCholesterol oxidase 1.1.3.6 0.665
1n4v FADCholesterol oxidase 1.1.3.6 0.665
1n4w FADCholesterol oxidase 1.1.3.6 0.665
2fkn NADUrocanate hydratase 4.2.1.49 0.665
2z6u SAHModification methylase HhaI 2.1.1.37 0.665
4rek FADCholesterol oxidase 1.1.3.6 0.665
4xxg FADCholesterol oxidase 1.1.3.6 0.665
5bp9 SAHPutative methyltransferase protein / 0.665
1b4v FADCholesterol oxidase 1.1.3.6 0.664
4u2t FADCholesterol oxidase 1.1.3.6 0.664
4xwr FADCholesterol oxidase 1.1.3.6 0.664
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.662
2gew FADCholesterol oxidase 1.1.3.6 0.662
2p35 SAHTrans-aconitate 2-methyltransferase / 0.662
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.662
1jkf NADInositol-3-phosphate synthase 5.5.1.4 0.661
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.661
2hmy SAMModification methylase HhaI 2.1.1.37 0.661
3gyj FADCholesterol oxidase 1.1.3.6 0.661
1n4u FAECholesterol oxidase 1.1.3.6 0.660
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.660
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.660
2oy0 SAHGenome polyprotein / 0.660
3wv8 ATPHmd co-occurring protein HcgE / 0.660
4c03 SFGProtein arginine N-methyltransferase 6 / 0.660
2xdo FADTetX family tetracycline inactivation enzyme / 0.659
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.659
3lcc SAHThiocyanate methyltransferase 1 / 0.658
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.657
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.657
4u2l SFDCholesterol oxidase 1.1.3.6 0.657
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.656
2v7g NADUrocanate hydratase 4.2.1.49 0.656
3kkz SAMUncharacterized protein / 0.656
4guu FA9Lysine-specific histone demethylase 1B 1 0.656
1aqi SAHModification methylase TaqI 2.1.1.72 0.655
5jjr SAHGenome polyprotein / 0.655
3dh0 SAMUncharacterized protein / 0.654
5epe SAHUncharacterized protein / 0.654
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.653
1x15 NADNAD(P) transhydrogenase subunit alpha 1.6.1.2 0.653
2hms NAIKtr system potassium uptake protein A / 0.652
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.652
3c3y SAHO-methyltransferase / 0.652
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.652
3rfx NADUronate dehydrogenase / 0.652
4gf5 SAHCalS11 / 0.652
2hnk SAHSAM-dependent O-methyltransferase / 0.651
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.651
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.651
4tm1 FDAKtzI / 0.651
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.651
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.651
5mht SAHModification methylase HhaI 2.1.1.37 0.651
1e3w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.650
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.650
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.650
4k39 SAMAnaerobic sulfatase-maturating enzyme 1.8.98 0.650