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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
1f3l SAH Protein arginine N-methyltransferase 3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1f3l SAHProtein arginine N-methyltransferase 3 / 1.206
2y1x SAHHistone-arginine methyltransferase CARM1 / 1.010
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.938
4lwp SAHArginine N-methyltransferase, putative / 0.925
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.919
4c03 SFGProtein arginine N-methyltransferase 6 / 0.908
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.902
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.893
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.887
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.883
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.861
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.854
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.846
5je2 SAHMethyl transferase / 0.824
4hh4 SAHCcbJ / 0.806
5jdz SAHMethyl transferase / 0.804
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.799
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.775
5je3 SAHMethyl transferase / 0.775
3go4 SAHUncharacterized protein / 0.772
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.771
2qe6 SAMUncharacterized protein / 0.760
4qpp SAHProtein arginine N-methyltransferase 6 / 0.755
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.754
5je4 SAHMethyl transferase / 0.753
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.751
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.750
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.747
5bp9 SAHPutative methyltransferase protein / 0.746
5bxy SAHPutative RNA methylase family UPF0020 / 0.746
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.745
2gs9 SAHUncharacterized protein / 0.742
3fri SAH16S rRNA methylase / 0.741
4nec SAHPutative SAM-dependent methyltransferase / 0.741
3lby SAHUncharacterized protein / 0.740
3ou2 SAHSAM-dependent methyltransferase / 0.740
1orh SAHProtein arginine N-methyltransferase 1 / 0.737
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.736
3lcc SAHThiocyanate methyltransferase 1 / 0.735
2yqz SAMUncharacterized protein / 0.733
5f2k SAHUncharacterized protein / 0.730
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.729
3p9k SAHCaffeic acid O-methyltransferase / 0.728
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.727
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.727
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.725
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.725
4kwc SAHMethyltransferase domain family / 0.725
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.724
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.723
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.722
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.719
1ori SAHProtein arginine N-methyltransferase 1 / 0.717
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.717
4c04 SFGProtein arginine N-methyltransferase 6 / 0.717
4rvd SAMD-mycarose 3-C-methyltransferase / 0.717
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.717
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.717
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.716
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.714
3e8s SAHUncharacterized protein / 0.713
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.710
3ha3 SAHHydroxymycolate synthase MmaA4 2.1.1 0.710
2xvm SAHTellurite methyltransferase 2.1.1.265 0.709
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.709
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.708
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.708
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.707
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.707
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.707
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.706
3tos SAHCalS11 / 0.706
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.705
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.705
1x1c SAHC-20 methyltransferase / 0.703
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.703
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.702
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.702
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.700
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.699
4x3q SAHSibL / 0.699
3bwc SAMSpermidine synthase, putative / 0.698
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.698
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.697
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.696
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.695
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.695
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.694
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.694
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.693
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.693
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.691
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.691
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.691
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.690
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.690
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.690
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.688
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.687
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.686
2zfu SAHRibosomal RNA-processing protein 8 / 0.686
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.686
4yv2 S4MSpermidine synthase, putative / 0.685
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.683
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.683
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.683
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.682
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.682
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.681
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.681
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.681
1sg9 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.680
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.679
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.678
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.678
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.678
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.678
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.677
3lst SAHCalO1 / 0.677
2g1p SAHDNA adenine methylase 2.1.1.72 0.676
2i9k SAHModification methylase HhaI 2.1.1.37 0.676
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.676
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.674
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.674
1x1a SAMC-20 methyltransferase / 0.674
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.674
3gu3 SAHMethyltransferase / 0.674
2o06 MTASpermidine synthase 2.5.1.16 0.672
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.672
4kvz SAHPtnL protein / 0.672
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.671
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.670
1x1b SAHC-20 methyltransferase / 0.669
2hnk SAHSAM-dependent O-methyltransferase / 0.669
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.668
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.668
4fr0 SAMArsenic methyltransferase / 0.668
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.667
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.667
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.667
4e2x SAHMethyltransferase / 0.667
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.666
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.665
4dmg SAMUncharacterized protein / 0.664
4pne SAHMethyltransferase-like protein / 0.664
3dh0 SAMUncharacterized protein / 0.663
1x1d SAHC-20 methyltransferase / 0.662
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.662
3cbg SAHO-methyltransferase / 0.662
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.662
2yxl SFG450aa long hypothetical fmu protein / 0.661
2z6u SAHModification methylase HhaI 2.1.1.37 0.661
3q60 ATPRhoptry protein 5B / 0.661
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.661
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.660
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.660
3tr6 SAHO-methyltransferase / 0.660
1h6c NDPGlucose--fructose oxidoreductase 1.1.99.28 0.659
1ryd NDPGlucose--fructose oxidoreductase 1.1.99.28 0.659
2zcj SAHModification methylase HhaI 2.1.1.37 0.659
3p9c SAHCaffeic acid O-methyltransferase / 0.659
4yv1 S4MSpermidine synthase, putative / 0.659
5d4v SAHUncharacterized protein MJ0489 / 0.659
4qnv GEKtRNA U34 carboxymethyltransferase / 0.657
9mht SAHModification methylase HhaI 2.1.1.37 0.657
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.656
5f8f SFGPossible transcriptional regulatory protein / 0.656
4bmz MTAAminodeoxyfutalosine nucleosidase / 0.655
1b38 ATPCyclin-dependent kinase 2 2.7.11.22 0.654
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.654
4qnu GEKtRNA U34 carboxymethyltransferase / 0.654
1wy7 SAHUncharacterized protein / 0.653
3iv6 SAMUncharacterized protein / 0.653
3ua3 SAHProtein arginine N-methyltransferase 5 / 0.652
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.651
2p35 SAHTrans-aconitate 2-methyltransferase / 0.651
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.650
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.650
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.650
3ou7 SAMSAM-dependent methyltransferase / 0.650
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.650
5bp7 SAHSAM-dependent methyltransferase / 0.650