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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
3t7s SAM Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3t7s SAMUncharacterized protein / 1.026
3kkz SAMUncharacterized protein / 0.976
3t0i SAHPutative methyltransferase / 0.970
3sxj SAMPutative methyltransferase / 0.925
3t7t SAHUncharacterized protein / 0.863
4hh4 SAHCcbJ / 0.858
2yqz SAMUncharacterized protein / 0.817
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.816
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.810
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.809
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.806
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.799
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.796
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.796
5bp9 SAHPutative methyltransferase protein / 0.792
5epe SAHUncharacterized protein / 0.785
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.779
4uy6 SAHHistidine N-alpha-methyltransferase / 0.778
3lst SAHCalO1 / 0.777
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.775
5je2 SAHMethyl transferase / 0.773
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.771
3e23 SAMUncharacterized protein / 0.770
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.769
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.769
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.768
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.760
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.759
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.759
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.756
5je3 SAHMethyl transferase / 0.756
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.755
3fri SAH16S rRNA methylase / 0.752
2xvm SAHTellurite methyltransferase 2.1.1.265 0.751
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.751
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.750
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.750
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.749
5bp7 SAHSAM-dependent methyltransferase / 0.748
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.747
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.745
3e8s SAHUncharacterized protein / 0.744
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.743
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.742
5jdz SAHMethyl transferase / 0.741
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.739
2zfu SAHRibosomal RNA-processing protein 8 / 0.737
2qe6 SAMUncharacterized protein / 0.735
3lcc SAHThiocyanate methyltransferase 1 / 0.734
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.732
4c04 SFGProtein arginine N-methyltransferase 6 / 0.725
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.723
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.722
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.721
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.720
4kvz SAHPtnL protein / 0.719
3go4 SAHUncharacterized protein / 0.718
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.717
5bxy SAHPutative RNA methylase family UPF0020 / 0.717
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.717
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.717
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.716
3p9k SAHCaffeic acid O-methyltransferase / 0.716
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.714
4x3q SAHSibL / 0.714
2p35 SAHTrans-aconitate 2-methyltransferase / 0.713
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.710
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.709
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.708
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.708
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.706
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.705
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.704
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.704
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.701
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.701
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.700
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.699
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.699
5je4 SAHMethyl transferase / 0.696
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.695
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.694
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.694
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.691
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.690
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.690
4qpp SAHProtein arginine N-methyltransferase 6 / 0.690
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.689
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.689
2gs9 SAHUncharacterized protein / 0.687
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.687
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.683
4dmg SAMUncharacterized protein / 0.681
4qnv GEKtRNA U34 carboxymethyltransferase / 0.680
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.679
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.677
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.675
4c03 SFGProtein arginine N-methyltransferase 6 / 0.675
4qnu GEKtRNA U34 carboxymethyltransferase / 0.675
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.674
3tza TZGGlutamate receptor 2 / 0.674
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.673
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.672
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.671
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.671
7mht SAHModification methylase HhaI 2.1.1.37 0.671
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.670
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.670
4e2x SAHMethyltransferase / 0.670
4ie0 PD2Alpha-ketoglutarate-dependent dioxygenase FTO / 0.670
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.669
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.669
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.669
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.669
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.668
5f8f SFGPossible transcriptional regulatory protein / 0.667
2c7q SAHModification methylase HhaI 2.1.1.37 0.666
2ibt NEAModification methylase TaqI 2.1.1.72 0.666
2wky IBCGlutamate receptor ionotropic, kainate 1 / 0.666
3h03 UBPGlutamate receptor 2 / 0.666
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.666
1orh SAHProtein arginine N-methyltransferase 1 / 0.665
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.664
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.663
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.662
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.662
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.662
2tpl HPPTyrosine phenol-lyase 4.1.99.2 0.661
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.661
3ou2 SAHSAM-dependent methyltransferase / 0.661
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.660
1y9d FADPyruvate oxidase 1.2.3.3 0.660
3kfm KAIGlutamate receptor 4 / 0.660
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.659
3r6c 17NAnthranilate phosphoribosyltransferase / 0.659
4bb3 KKAIsopenicillin N synthase 1.21.3.1 0.659
3c34 KAIGlutamate receptor ionotropic, kainate 1 / 0.658
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.658
4yv0 S4MSpermidine synthase, putative / 0.658
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.657
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.657
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.657
3c36 KAIGlutamate receptor ionotropic, kainate 1 / 0.656
1hb3 SCVIsopenicillin N synthase 1.21.3.1 0.655
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.655
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.655
3mht SAHModification methylase HhaI 2.1.1.37 0.655
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.655
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.654
4dld TZGGlutamate receptor ionotropic, kainate 1 / 0.654
5f2k SAHUncharacterized protein / 0.654
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.653
2i9k SAHModification methylase HhaI 2.1.1.37 0.653
3p8z SAHGenome polyprotein 2.1.1.56 0.653
1wy7 SAHUncharacterized protein / 0.652
2r59 PH0Leukotriene A-4 hydrolase 3.3.2.6 0.652
3cbg SAHO-methyltransferase / 0.652
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.651
1ori SAHProtein arginine N-methyltransferase 1 / 0.651
1u5a BIKL-lactate dehydrogenase 1.1.1.27 0.650
4pgh SAMCaffeic acid O-methyltransferase / 0.650