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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
5bp9 SAH Putative methyltransferase protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5bp9 SAHPutative methyltransferase protein / 1.062
3fri SAH16S rRNA methylase / 0.852
2yqz SAMUncharacterized protein / 0.822
5je3 SAHMethyl transferase / 0.794
3t7s SAMUncharacterized protein / 0.792
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.789
3lcc SAHThiocyanate methyltransferase 1 / 0.789
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.787
5jdz SAHMethyl transferase / 0.787
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.781
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.779
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.779
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.776
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.775
5je2 SAHMethyl transferase / 0.775
4c04 SFGProtein arginine N-methyltransferase 6 / 0.774
3kkz SAMUncharacterized protein / 0.772
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.771
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.770
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.769
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.767
4c03 SFGProtein arginine N-methyltransferase 6 / 0.767
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.765
4hh4 SAHCcbJ / 0.764
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.761
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.760
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.760
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.758
3go4 SAHUncharacterized protein / 0.752
4qpp SAHProtein arginine N-methyltransferase 6 / 0.748
1f3l SAHProtein arginine N-methyltransferase 3 / 0.746
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.744
4nec SAHPutative SAM-dependent methyltransferase / 0.744
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.738
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.737
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.737
4e2x SAHMethyltransferase / 0.736
3t0i SAHPutative methyltransferase / 0.734
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.733
3e8s SAHUncharacterized protein / 0.733
4lwp SAHArginine N-methyltransferase, putative / 0.733
4uy6 SAHHistidine N-alpha-methyltransferase / 0.731
5bxy SAHPutative RNA methylase family UPF0020 / 0.731
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.729
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.728
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.727
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.725
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.724
5je4 SAHMethyl transferase / 0.723
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.722
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.722
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.719
2qe6 SAMUncharacterized protein / 0.719
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.719
3t7t SAHUncharacterized protein / 0.719
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.718
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.717
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.717
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.717
4rvd SAMD-mycarose 3-C-methyltransferase / 0.716
2zfu SAHRibosomal RNA-processing protein 8 / 0.715
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.715
2p35 SAHTrans-aconitate 2-methyltransferase / 0.713
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.713
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.713
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.710
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.708
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.708
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.706
4x3q SAHSibL / 0.706
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.705
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.705
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.705
2gs9 SAHUncharacterized protein / 0.704
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.702
4yuz S4MSpermidine synthase, putative / 0.702
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.701
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.701
4pne SAHMethyltransferase-like protein / 0.701
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.700
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.699
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.699
1ori SAHProtein arginine N-methyltransferase 1 / 0.698
1boo SAHModification methylase PvuII 2.1.1.113 0.697
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.696
2hnk SAHSAM-dependent O-methyltransferase / 0.695
3lst SAHCalO1 / 0.695
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.695
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.695
4kwc SAHMethyltransferase domain family / 0.694
2i9k SAHModification methylase HhaI 2.1.1.37 0.691
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.691
3cbg SAHO-methyltransferase / 0.690
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.690
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.689
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.687
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.687
10mh SAHModification methylase HhaI 2.1.1.37 0.686
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.686
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.686
3tr6 SAHO-methyltransferase / 0.686
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.685
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.685
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.684
3bwc SAMSpermidine synthase, putative / 0.684
4kvz SAHPtnL protein / 0.684
3sxj SAMPutative methyltransferase / 0.682
4oa5 SAHO-methyltransferase family protein / 0.682
5f2k SAHUncharacterized protein / 0.682
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.681
7mht SAHModification methylase HhaI 2.1.1.37 0.681
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.680
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.680
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.679
3ou2 SAHSAM-dependent methyltransferase / 0.679
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.678
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.677
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.677
1orh SAHProtein arginine N-methyltransferase 1 / 0.676
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.676
3p9k SAHCaffeic acid O-methyltransferase / 0.676
2xxy KAIGlutamate receptor ionotropic, kainate 2 / 0.675
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.675
4bdo KAIGlutamate receptor ionotropic, kainate 2 / 0.675
3p9c SAHCaffeic acid O-methyltransferase / 0.674
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.674
3c36 KAIGlutamate receptor ionotropic, kainate 1 / 0.673
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.673
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.673
5bp7 SAHSAM-dependent methyltransferase / 0.673
2ibt NEAModification methylase TaqI 2.1.1.72 0.672
9mht SAHModification methylase HhaI 2.1.1.37 0.672
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.671
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.670
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.669
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.669
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.668
3c3y SAHO-methyltransferase / 0.667
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.666
3iv6 SAMUncharacterized protein / 0.666
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.666
4qnv GEKtRNA U34 carboxymethyltransferase / 0.666
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.666
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.665
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.665
4fr0 SAMArsenic methyltransferase / 0.665
4qnu GEKtRNA U34 carboxymethyltransferase / 0.665
4yv2 S4MSpermidine synthase, putative / 0.665
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.664
2ore SAHDNA adenine methylase 2.1.1.72 0.664
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.664
4yv0 S4MSpermidine synthase, putative / 0.664
1x1c SAHC-20 methyltransferase / 0.663
2uyh SAHModification methylase HhaI 2.1.1.37 0.663
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.663
2pbw DOQGlutamate receptor ionotropic, kainate 1 / 0.662
2xxv KAIGlutamate receptor ionotropic, kainate 2 / 0.662
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.661
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.661
4bdr KAIGlutamate receptor ionotropic, kainate 2 / 0.661
4f3g KAIGlutamate receptor 3 / 0.661
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.660
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.660
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.660
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.659
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.659
3c34 KAIGlutamate receptor ionotropic, kainate 1 / 0.659
3eey SAMrRNA methylase / 0.659
5epe SAHUncharacterized protein / 0.659
1w06 W05Isopenicillin N synthase 1.21.3.1 0.658
3c35 KAIGlutamate receptor ionotropic, kainate 1 / 0.658
1blz ACVIsopenicillin N synthase 1.21.3.1 0.657
3rib SAHN-lysine methyltransferase SMYD2 / 0.657
3zoi M2WIsopenicillin N synthase 1.21.3.1 0.657
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.657
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.657
1obn ASVIsopenicillin N synthase 1.21.3.1 0.655
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.655
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.654
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.654
4pgh SAMCaffeic acid O-methyltransferase / 0.654
1bk0 ACVIsopenicillin N synthase 1.21.3.1 0.653
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.653
1u5a BIKL-lactate dehydrogenase 1.1.1.27 0.652
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.652
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.650
3kfm KAIGlutamate receptor 4 / 0.650
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.650