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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
3t0i SAH Putative methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3t0i SAHPutative methyltransferase / 1.029
3t7s SAMUncharacterized protein / 0.970
3sxj SAMPutative methyltransferase / 0.954
3kkz SAMUncharacterized protein / 0.927
3t7t SAHUncharacterized protein / 0.842
4c03 SFGProtein arginine N-methyltransferase 6 / 0.780
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.775
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.764
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.757
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.755
2yqz SAMUncharacterized protein / 0.753
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.752
3p9k SAHCaffeic acid O-methyltransferase / 0.747
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.746
3e8s SAHUncharacterized protein / 0.744
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.742
4uy6 SAHHistidine N-alpha-methyltransferase / 0.742
3e23 SAMUncharacterized protein / 0.741
3lst SAHCalO1 / 0.741
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.740
5bp9 SAHPutative methyltransferase protein / 0.734
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.733
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.729
3fri SAH16S rRNA methylase / 0.724
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.717
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.717
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.714
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.710
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.710
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.707
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.705
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.704
2xvm SAHTellurite methyltransferase 2.1.1.265 0.704
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.697
5je2 SAHMethyl transferase / 0.697
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.694
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.694
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.693
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.692
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.692
2zfu SAHRibosomal RNA-processing protein 8 / 0.691
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.689
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.688
4c04 SFGProtein arginine N-methyltransferase 6 / 0.687
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.687
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.686
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.686
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.685
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.683
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.682
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.682
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.681
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.680
5bxy SAHPutative RNA methylase family UPF0020 / 0.679
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.678
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.678
4pne SAHMethyltransferase-like protein / 0.678
1orh SAHProtein arginine N-methyltransferase 1 / 0.676
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.673
4x3q SAHSibL / 0.673
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.673
5epe SAHUncharacterized protein / 0.672
1vso AT1Glutamate receptor ionotropic, kainate 1 / 0.671
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.671
4hh4 SAHCcbJ / 0.671
3c34 KAIGlutamate receptor ionotropic, kainate 1 / 0.669
3fvu IACKynurenine--oxoglutarate transaminase 1 2.6.1.7 0.669
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.668
4kvz SAHPtnL protein / 0.668
4dmg SAMUncharacterized protein / 0.666
4ie0 PD2Alpha-ketoglutarate-dependent dioxygenase FTO / 0.666
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.666
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.665
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.665
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.664
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.663
2e77 FMNLactate oxidase / 0.662
2nli FMNLactate oxidase / 0.662
3c36 KAIGlutamate receptor ionotropic, kainate 1 / 0.662
3ou2 SAHSAM-dependent methyltransferase / 0.662
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.661
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.661
5f8f SFGPossible transcriptional regulatory protein / 0.661
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.660
3h03 UBPGlutamate receptor 2 / 0.660
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.660
3lcc SAHThiocyanate methyltransferase 1 / 0.659
3zku HCVIsopenicillin N synthase 1.21.3.1 0.659
5bp7 SAHSAM-dependent methyltransferase / 0.659
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.658
5jdz SAHMethyl transferase / 0.658
2p1o NLAProtein TRANSPORT INHIBITOR RESPONSE 1 / 0.657
2wba NDPTrypanothione reductase 1.8.1.12 0.656
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.655
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.655
1ori SAHProtein arginine N-methyltransferase 1 / 0.654
2qs3 UBEGlutamate receptor ionotropic, kainate 1 / 0.654
4ao4 PLKBeta-transaminase / 0.654
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.654
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.654
2qe6 SAMUncharacterized protein / 0.653
3kfm KAIGlutamate receptor 4 / 0.653
4f3g KAIGlutamate receptor 3 / 0.653
4lwp SAHArginine N-methyltransferase, putative / 0.653
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.652
3mht SAHModification methylase HhaI 2.1.1.37 0.652
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.652
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.651
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.651
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.651
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.650