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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
2v74 SAH Histone-arginine methyltransferase CARM1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2v74 SAHHistone-arginine methyltransferase CARM1 / 1.157
3b3f SAHHistone-arginine methyltransferase CARM1 / 1.003
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.943
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.939
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.937
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.926
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.901
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.897
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.889
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.863
4c03 SFGProtein arginine N-methyltransferase 6 / 0.853
1f3l SAHProtein arginine N-methyltransferase 3 / 0.846
4lwp SAHArginine N-methyltransferase, putative / 0.829
5bp9 SAHPutative methyltransferase protein / 0.789
2yqz SAMUncharacterized protein / 0.777
4qpp SAHProtein arginine N-methyltransferase 6 / 0.777
4hh4 SAHCcbJ / 0.776
3lcc SAHThiocyanate methyltransferase 1 / 0.775
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.775
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.761
5jdz SAHMethyl transferase / 0.761
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.750
2zfu SAHRibosomal RNA-processing protein 8 / 0.743
4c04 SFGProtein arginine N-methyltransferase 6 / 0.741
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.737
5je2 SAHMethyl transferase / 0.732
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.731
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.728
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.726
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.724
1x1b SAHC-20 methyltransferase / 0.723
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.720
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.720
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.716
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.716
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.714
3t7s SAMUncharacterized protein / 0.714
5je4 SAHMethyl transferase / 0.714
3fri SAH16S rRNA methylase / 0.713
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.712
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.709
5bxy SAHPutative RNA methylase family UPF0020 / 0.709
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.706
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.701
3go4 SAHUncharacterized protein / 0.700
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.700
4nec SAHPutative SAM-dependent methyltransferase / 0.700
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.699
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.698
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.697
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.697
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.697
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.695
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.695
4e2x SAHMethyltransferase / 0.692
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.690
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.690
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.690
2gs9 SAHUncharacterized protein / 0.688
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.688
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.688
5je3 SAHMethyl transferase / 0.688
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.687
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.687
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.686
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.686
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.686
4x3q SAHSibL / 0.686
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.685
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.685
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.684
3e8s SAHUncharacterized protein / 0.684
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.684
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.683
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.683
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.681
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.680
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.679
4rvd SAMD-mycarose 3-C-methyltransferase / 0.678
5bp7 SAHSAM-dependent methyltransferase / 0.678
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.676
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.675
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.673
2qe6 SAMUncharacterized protein / 0.673
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.672
3lby SAHUncharacterized protein / 0.672
3p9k SAHCaffeic acid O-methyltransferase / 0.672
3tos SAHCalS11 / 0.672
1x1d SAHC-20 methyltransferase / 0.671
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.671
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.671
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.671
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.670
1ori SAHProtein arginine N-methyltransferase 1 / 0.670
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.670
1orh SAHProtein arginine N-methyltransferase 1 / 0.669
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.669
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.669
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.669
1sg9 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.668
2ore SAHDNA adenine methylase 2.1.1.72 0.668
5eku SAHArginine N-methyltransferase, putative / 0.668
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.667
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.667
1x1c SAHC-20 methyltransferase / 0.667
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.667
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.667
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.666
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.666
3mht SAHModification methylase HhaI 2.1.1.37 0.666
3p9c SAHCaffeic acid O-methyltransferase / 0.666
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.665
3duw SAHO-methyltransferase, putative / 0.665
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.665
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.664
2z6u SAHModification methylase HhaI 2.1.1.37 0.663
4qnu GEKtRNA U34 carboxymethyltransferase / 0.662
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.660
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.659
4rtj SFGDNA adenine methylase 2.1.1.72 0.659
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.657
4rtk SAHDNA adenine methylase 2.1.1.72 0.657
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.656
3kkz SAMUncharacterized protein / 0.656
3t7t SAHUncharacterized protein / 0.656
3tm4 SAMUncharacterized protein / 0.656
3ua3 SAHProtein arginine N-methyltransferase 5 / 0.656
5epe SAHUncharacterized protein / 0.656
3dh0 SAMUncharacterized protein / 0.653
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.653
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.651
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.650
3t0i SAHPutative methyltransferase / 0.650
4ce0 SAHProbable O-methyltransferase / 0.650
7mht SAHModification methylase HhaI 2.1.1.37 0.650