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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
1ri3 SAH mRNA cap guanine-N7 methyltransferase 2.1.1.56

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.983
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.864
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.838
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.827
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.805
5jdz SAHMethyl transferase / 0.798
5je2 SAHMethyl transferase / 0.796
5je3 SAHMethyl transferase / 0.793
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.784
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.782
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.774
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.767
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.764
2yqz SAMUncharacterized protein / 0.763
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.763
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.746
3t7s SAMUncharacterized protein / 0.743
4qpp SAHProtein arginine N-methyltransferase 6 / 0.738
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.732
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.732
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.731
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.729
4nec SAHPutative SAM-dependent methyltransferase / 0.729
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.728
3fri SAH16S rRNA methylase / 0.724
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.721
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.717
3p9c SAHCaffeic acid O-methyltransferase / 0.716
5bxy SAHPutative RNA methylase family UPF0020 / 0.715
5bp9 SAHPutative methyltransferase protein / 0.710
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.709
3kkz SAMUncharacterized protein / 0.708
2np7 NEAModification methylase TaqI 2.1.1.72 0.707
2p35 SAHTrans-aconitate 2-methyltransferase / 0.707
2ibt NEAModification methylase TaqI 2.1.1.72 0.705
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.704
2o06 MTASpermidine synthase 2.5.1.16 0.703
1f3l SAHProtein arginine N-methyltransferase 3 / 0.702
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.701
3bwc SAMSpermidine synthase, putative / 0.700
4yuz S4MSpermidine synthase, putative / 0.697
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.696
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.696
3p9k SAHCaffeic acid O-methyltransferase / 0.695
3t7t SAHUncharacterized protein / 0.693
4qnv GEKtRNA U34 carboxymethyltransferase / 0.693
3go4 SAHUncharacterized protein / 0.690
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.690
4yv2 S4MSpermidine synthase, putative / 0.690
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.689
4qnu GEKtRNA U34 carboxymethyltransferase / 0.689
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.688
3dh0 SAMUncharacterized protein / 0.686
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.686
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.686
4yv1 S4MSpermidine synthase, putative / 0.686
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.684
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.683
2ih2 NEAModification methylase TaqI 2.1.1.72 0.682
3lst SAHCalO1 / 0.681
3rw9 DSHSpermidine synthase 2.5.1.16 0.681
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.681
5je4 SAHMethyl transferase / 0.681
4yuv S4MSpermidine synthase, putative / 0.680
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.679
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.679
4e2x SAHMethyltransferase / 0.679
2xvm SAHTellurite methyltransferase 2.1.1.265 0.678
4kvz SAHPtnL protein / 0.677
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.677
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.675
2pan FADGlyoxylate carboligase 4.1.1.47 0.675
2wsb NADGalactitol dehydrogenase / 0.675
2zfu SAHRibosomal RNA-processing protein 8 / 0.675
2pt6 S4MSpermidine synthase / 0.674
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.673
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.673
3ou2 SAHSAM-dependent methyltransferase / 0.673
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.673
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.671
4hh4 SAHCcbJ / 0.671
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.670
1i8t FADUDP-galactopyranose mutase 5.4.99.9 0.669
2eg5 SAH7-methylxanthosine synthase 1 / 0.669
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.669
2qe6 SAMUncharacterized protein / 0.669
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.669
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.669
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.669
4fr0 SAMArsenic methyltransferase / 0.669
4pgh SAMCaffeic acid O-methyltransferase / 0.669
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.668
3gu3 SAHMethyltransferase / 0.668
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.668
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.666
1x1b SAHC-20 methyltransferase / 0.666
4gbe SAHDNA adenine methylase 2.1.1.72 0.666
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.665
1orh SAHProtein arginine N-methyltransferase 1 / 0.664
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.664
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.663
4c04 SFGProtein arginine N-methyltransferase 6 / 0.663
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.663
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.661
3s55 NADPutative short-chain dehydrogenase/reductase / 0.661
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.661
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.660
3nug NADPyridoxal 4-dehydrogenase 1.1.1.107 0.660
4mb2 ATPUncharacterized protein / 0.660
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.659
2ewm NAD(S)-1-Phenylethanol dehydrogenase 1.1.1.311 0.659
2ih5 NEAModification methylase TaqI 2.1.1.72 0.659
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.659
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.659
3zdn FADMonoamine oxidase N 1.4.3.4 0.658
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.658
1pow FADPyruvate oxidase 1.2.3.3 0.657
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.657
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.656
3e23 SAMUncharacterized protein / 0.656
1hzz NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.655
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.655
3t0i SAHPutative methyltransferase / 0.655
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.655
4yac NAIC alpha-dehydrogenase / 0.655
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.655
2gs9 SAHUncharacterized protein / 0.654
1ori SAHProtein arginine N-methyltransferase 1 / 0.653
1yf3 SAHDNA adenine methylase / 0.653
3lcc SAHThiocyanate methyltransferase 1 / 0.653
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.653
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.653
5f8f SFGPossible transcriptional regulatory protein / 0.653
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.652
3ou6 SAMSAM-dependent methyltransferase / 0.652
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.652
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.651
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.651
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.651
1v0j FADUDP-galactopyranose mutase 5.4.99.9 0.650
2igo FADPyranose 2-oxidase / 0.650
2yxl SFG450aa long hypothetical fmu protein / 0.650
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.650
3pl8 FADPyranose 2-oxidase / 0.650