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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
4yuz S4M Spermidine synthase, putative

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4yuz S4MSpermidine synthase, putative / 1.144
4yv2 S4MSpermidine synthase, putative / 1.026
4yv1 S4MSpermidine synthase, putative / 0.979
4yuv S4MSpermidine synthase, putative / 0.974
4yv0 S4MSpermidine synthase, putative / 0.939
2pt6 S4MSpermidine synthase / 0.827
3bwc SAMSpermidine synthase, putative / 0.782
2o07 MTASpermidine synthase 2.5.1.16 0.776
1jq3 AATPolyamine aminopropyltransferase / 0.758
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.757
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.753
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.747
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.747
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.745
3tos SAHCalS11 / 0.745
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.743
1yf3 SAHDNA adenine methylase / 0.741
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.740
4nec SAHPutative SAM-dependent methyltransferase / 0.739
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.737
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.736
3ou6 SAMSAM-dependent methyltransferase / 0.735
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.733
2hmv ADPKtr system potassium uptake protein A / 0.731
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.724
5je3 SAHMethyl transferase / 0.724
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.722
5je4 SAHMethyl transferase / 0.722
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.720
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.716
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.714
4gf5 SAHCalS11 / 0.712
2g1p SAHDNA adenine methylase 2.1.1.72 0.709
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.706
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.705
3rw9 DSHSpermidine synthase 2.5.1.16 0.705
2pan FADGlyoxylate carboligase 4.1.1.47 0.704
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.703
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.703
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.703
5bp9 SAHPutative methyltransferase protein / 0.702
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.701
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.701
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.699
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.697
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.697
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.696
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.695
3cbg SAHO-methyltransferase / 0.695
1i3l NADUDP-glucose 4-epimerase / 0.694
2hms NAIKtr system potassium uptake protein A / 0.694
3wv8 ATPHmd co-occurring protein HcgE / 0.694
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.694
2p35 SAHTrans-aconitate 2-methyltransferase / 0.693
3mht SAHModification methylase HhaI 2.1.1.37 0.691
2c7q SAHModification methylase HhaI 2.1.1.37 0.690
2uyh SAHModification methylase HhaI 2.1.1.37 0.690
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.690
2pkm ADNAdenosine kinase 2.7.1.20 0.689
3wv7 ADPHmd co-occurring protein HcgE / 0.689
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.688
2z6u SAHModification methylase HhaI 2.1.1.37 0.688
2o06 MTASpermidine synthase 2.5.1.16 0.687
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.687
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.687
1y9d FADPyruvate oxidase 1.2.3.3 0.686
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.686
1wy7 SAHUncharacterized protein / 0.685
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.685
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.683
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.683
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.683
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.683
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.682
3fpf MTAUncharacterized protein / 0.682
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.681
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.681
4yac NAIC alpha-dehydrogenase / 0.681
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.680
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.680
7mht SAHModification methylase HhaI 2.1.1.37 0.680
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.678
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.678
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.677
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.677
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.677
4kwc SAHMethyltransferase domain family / 0.677
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.676
2yxl SFG450aa long hypothetical fmu protein / 0.674
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.671
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.670
3c3y SAHO-methyltransferase / 0.670
3h5n ATPMccB protein / 0.670
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.670
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.669
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.669
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.668
2yqz SAMUncharacterized protein / 0.668
3dh0 SAMUncharacterized protein / 0.668
4eaj ATP5'-AMP-activated protein kinase subunit gamma-1 / 0.668
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.667
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.666
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.666
3tm4 SAMUncharacterized protein / 0.666
4a99 FADTetX family tetracycline inactivation enzyme / 0.666
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.664
1mxt FAECholesterol oxidase 1.1.3.6 0.664
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.664
3r6t LU1Catechol O-methyltransferase 2.1.1.6 0.664
3s5w FADL-ornithine N(5)-monooxygenase / 0.664
3uq9 TBNPutative adenosine kinase / 0.664
4j33 FADKynurenine 3-monooxygenase / 0.664
1b4v FADCholesterol oxidase 1.1.3.6 0.663
1hzz NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.663
1n1p FADCholesterol oxidase 1.1.3.6 0.663
1n4v FADCholesterol oxidase 1.1.3.6 0.663
1n4w FADCholesterol oxidase 1.1.3.6 0.663
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.663
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.663
3hvi 619Catechol O-methyltransferase 2.1.1.6 0.663
4rek FADCholesterol oxidase 1.1.3.6 0.663
4xxg FADCholesterol oxidase 1.1.3.6 0.663
1g1a NADdTDP-glucose 4,6-dehydratase / 0.662
4kvz SAHPtnL protein / 0.662
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.661
3lcc SAHThiocyanate methyltransferase 1 / 0.661
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.661
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.660
3nwe 662Catechol O-methyltransferase 2.1.1.6 0.660
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.660
1b8s FADCholesterol oxidase 1.1.3.6 0.659
2gs9 SAHUncharacterized protein / 0.659
2xdo FADTetX family tetracycline inactivation enzyme / 0.659
2zcj SAHModification methylase HhaI 2.1.1.37 0.659
3rfx NADUronate dehydrogenase / 0.659
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.659
9mht SAHModification methylase HhaI 2.1.1.37 0.659
2dki FAD3-hydroxybenzoate 4-monooxygenase 1.14.13.23 0.658
3cnj FADCholesterol oxidase 1.1.3.6 0.658
3gyi FADCholesterol oxidase 1.1.3.6 0.658
5jla NADPutative short-chain dehydrogenase/reductase / 0.658
1jkf NADInositol-3-phosphate synthase 5.5.1.4 0.657
2cdu ADPNADH oxidase / 0.657
2ewm NAD(S)-1-Phenylethanol dehydrogenase 1.1.1.311 0.657
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.657
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.657
3aw9 NADNAD-dependent epimerase/dehydratase / 0.657
3cox FADCholesterol oxidase 1.1.3.6 0.656
3lby SAHUncharacterized protein / 0.656
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.656
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.656
4y9d NAIC alpha-dehydrogenase / 0.656
1g60 SAMModification methylase MboII 2.1.1.72 0.655
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.655
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.655
4g56 SAHProtein arginine N-methyltransferase 5 / 0.655
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.654
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.653
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.653
3qv2 SAH5-cytosine DNA methyltransferase / 0.653
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.653
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.652
1l7e NAINAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.652
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.652
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.651
2oo5 TXDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.651
3duw SAHO-methyltransferase, putative / 0.651
3ldf SAHUncharacterized protein / 0.651
3ozt OZZCatechol O-methyltransferase 2.1.1.6 0.651
4dc3 2FAPutative adenosine kinase / 0.651
4eak ATP5'-AMP-activated protein kinase subunit gamma-1 / 0.651
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.651
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.650
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.650
4c04 SFGProtein arginine N-methyltransferase 6 / 0.650
4nzh FADL-ornithine N(5)-monooxygenase / 0.650
4u8i FDAUDP-galactopyranose mutase / 0.650