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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
1y8q ATP SUMO-activating enzyme subunit 2 6.3.2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 1.113
4d79 ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.747
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.746
3lcc SAHThiocyanate methyltransferase 1 / 0.745
4yuz S4MSpermidine synthase, putative / 0.745
4nec SAHPutative SAM-dependent methyltransferase / 0.731
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.727
3wv8 ATPHmd co-occurring protein HcgE / 0.722
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.720
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.719
3wv7 ADPHmd co-occurring protein HcgE / 0.719
2p35 SAHTrans-aconitate 2-methyltransferase / 0.717
3h5n ATPMccB protein / 0.717
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.716
5je4 SAHMethyl transferase / 0.714
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.713
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.712
4yv2 S4MSpermidine synthase, putative / 0.711
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.710
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.710
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.709
1skm SAHModification methylase HhaI 2.1.1.37 0.708
2c7q SAHModification methylase HhaI 2.1.1.37 0.708
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.708
5jdz SAHMethyl transferase / 0.708
5je3 SAHMethyl transferase / 0.708
1g1a NADdTDP-glucose 4,6-dehydratase / 0.705
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.705
5bp9 SAHPutative methyltransferase protein / 0.705
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.704
2fkn NADUrocanate hydratase 4.2.1.49 0.704
3mht SAHModification methylase HhaI 2.1.1.37 0.704
2uyh SAHModification methylase HhaI 2.1.1.37 0.703
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.701
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.699
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.698
2hmv ADPKtr system potassium uptake protein A / 0.697
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.695
2yy7 NADL-threonine dehydrogenase / 0.694
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.693
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.693
3n1s 5GPPurine nucleoside phosphoramidase / 0.693
4yac NAIC alpha-dehydrogenase / 0.693
5d4v SAHUncharacterized protein MJ0489 / 0.692
7mht SAHModification methylase HhaI 2.1.1.37 0.691
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.690
3c3y SAHO-methyltransferase / 0.689
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.689
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.689
4kvz SAHPtnL protein / 0.689
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.687
2yxl SFG450aa long hypothetical fmu protein / 0.687
3ou2 SAHSAM-dependent methyltransferase / 0.687
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.687
4rdi ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.686
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.686
1uay ADNOxidoreductase / 0.685
3ldf SAHUncharacterized protein / 0.685
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.685
1u28 NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.684
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.683
3bwc SAMSpermidine synthase, putative / 0.683
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.683
3tos SAHCalS11 / 0.683
2fsv NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.682
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.682
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.681
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.681
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.681
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.681
3s5w FADL-ornithine N(5)-monooxygenase / 0.681
1f8g NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.680
3rfx NADUronate dehydrogenase / 0.680
2pan FADGlyoxylate carboligase 4.1.1.47 0.679
2v7g NADUrocanate hydratase 4.2.1.49 0.679
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.677
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.677
2br5 SAHCephalosporin hydroxylase CmcI / 0.677
2oor NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.676
3ldg SAHUncharacterized protein / 0.676
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.675
3go4 SAHUncharacterized protein / 0.675
9mht SAHModification methylase HhaI 2.1.1.37 0.675
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.674
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.674
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.673
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.673
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.671
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.671
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.671
1y9d FADPyruvate oxidase 1.2.3.3 0.670
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.670
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.669
2o06 MTASpermidine synthase 2.5.1.16 0.669
2o07 MTASpermidine synthase 2.5.1.16 0.669
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.669
4rtr SAMDNA adenine methylase 2.1.1.72 0.669
4yv1 S4MSpermidine synthase, putative / 0.669
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.668
1yf3 SAHDNA adenine methylase / 0.668
3fpf MTAUncharacterized protein / 0.668
4y9d NAIC alpha-dehydrogenase / 0.668
2ore SAHDNA adenine methylase 2.1.1.72 0.667
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.667
3l8k ADPDihydrolipoamide dehydrogenase (PdhD-3) / 0.667
4rtj SFGDNA adenine methylase 2.1.1.72 0.667
2hms NAIKtr system potassium uptake protein A / 0.666
2pt6 S4MSpermidine synthase / 0.666
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.666
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.666
1boo SAHModification methylase PvuII 2.1.1.113 0.665
2rgh FADAlpha-Glycerophosphate Oxidase / 0.665
3cbg SAHO-methyltransferase / 0.665
3nwe 662Catechol O-methyltransferase 2.1.1.6 0.665
3wle NAD(R)-specific carbonyl reductase / 0.665
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.665
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.664
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.664
1av5 AP2Histidine triad nucleotide-binding protein 1 3 0.663
1l7e NAINAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.663
3icp NADNAD-dependent epimerase/dehydratase / 0.663
3ics FADCoenzyme A disulfide reductase / 0.663
1zmd NAIDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.662
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.662
4c4o NADSADH / 0.662
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.662
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.661
1yqz FADCoenzyme A disulfide reductase / 0.661
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.661
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.661
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.660
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.660
2qa2 FADPolyketide oxygenase CabE / 0.660
3he3 FADUDP-galactopyranose mutase / 0.660
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.659
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.658
1hku NADC-terminal-binding protein 1 1.1.1 0.658
1zem NADXylitol dehydrogenase / 0.658
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.658
3ou7 SAMSAM-dependent methyltransferase / 0.658
3ozt OZZCatechol O-methyltransferase 2.1.1.6 0.658
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.657
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.657
3atq FDAConserved Archaeal protein / 0.657
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.657
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.657
1nw5 SAMModification methylase RsrI 2.1.1.72 0.656
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.656
3ec7 NADInositol 2-dehydrogenase / 0.656
3ruh NADUDP-N-acetylglucosamine 4-epimerase / 0.656
1z5c ADPType 2 DNA topoisomerase 6 subunit B / 0.655
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.655
1g60 SAMModification methylase MboII 2.1.1.72 0.654
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.654
1rzy 5ASHistidine triad nucleotide-binding protein 1 3 0.654
1v59 NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.653
1zq9 SAMProbable dimethyladenosine transferase / 0.653
4rtk SAHDNA adenine methylase 2.1.1.72 0.653
4tm3 FADKtzI / 0.653
4gbe SAHDNA adenine methylase 2.1.1.72 0.652
4rvd SAMD-mycarose 3-C-methyltransferase / 0.652
2yqz SAMUncharacterized protein / 0.651
4b69 FADL-ornithine N(5)-monooxygenase / 0.651
4yuv S4MSpermidine synthase, putative / 0.651
1joa FADNADH peroxidase 1.11.1.1 0.650
3grs FADGlutathione reductase, mitochondrial 1.8.1.7 0.650
3int FDAUDP-galactopyranose mutase 5.4.99.9 0.650
3nta FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.650
3r6t LU1Catechol O-methyltransferase 2.1.1.6 0.650