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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
5je3 SAH Methyl transferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
5je3 SAHMethyl transferase / 1.062
5jdz SAHMethyl transferase / 1.056
5je2 SAHMethyl transferase / 0.960
5je4 SAHMethyl transferase / 0.946
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.847
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.845
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.844
4c03 SFGProtein arginine N-methyltransferase 6 / 0.829
4qpp SAHProtein arginine N-methyltransferase 6 / 0.828
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.821
4c04 SFGProtein arginine N-methyltransferase 6 / 0.818
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.813
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.812
3fri SAH16S rRNA methylase / 0.803
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.797
1orh SAHProtein arginine N-methyltransferase 1 / 0.795
3lcc SAHThiocyanate methyltransferase 1 / 0.795
5bp9 SAHPutative methyltransferase protein / 0.794
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.793
4lwp SAHArginine N-methyltransferase, putative / 0.793
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.791
1ve3 SAMUncharacterized protein / 0.789
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.785
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.785
2qe6 SAMUncharacterized protein / 0.784
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.783
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.781
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.780
5bxy SAHPutative RNA methylase family UPF0020 / 0.778
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.778
3go4 SAHUncharacterized protein / 0.777
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.777
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.776
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.776
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.776
1f3l SAHProtein arginine N-methyltransferase 3 / 0.775
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.774
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.774
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.768
2p35 SAHTrans-aconitate 2-methyltransferase / 0.767
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.767
1ori SAHProtein arginine N-methyltransferase 1 / 0.763
2yqz SAMUncharacterized protein / 0.762
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.762
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.761
4nec SAHPutative SAM-dependent methyltransferase / 0.760
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.758
2ibt NEAModification methylase TaqI 2.1.1.72 0.756
3t7s SAMUncharacterized protein / 0.756
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.756
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.756
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.754
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.752
2np7 NEAModification methylase TaqI 2.1.1.72 0.751
2xvm SAHTellurite methyltransferase 2.1.1.265 0.750
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.749
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.747
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.744
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.743
2ih2 NEAModification methylase TaqI 2.1.1.72 0.739
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.735
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.735
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.734
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.732
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.728
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.727
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.727
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.725
2gs9 SAHUncharacterized protein / 0.724
4yuz S4MSpermidine synthase, putative / 0.724
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.723
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.721
2yxl SFG450aa long hypothetical fmu protein / 0.721
2o06 MTASpermidine synthase 2.5.1.16 0.718
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.718
4rtk SAHDNA adenine methylase 2.1.1.72 0.718
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.717
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.716
2g1p SAHDNA adenine methylase 2.1.1.72 0.714
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.714
3ldg SAHUncharacterized protein / 0.714
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.712
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.710
2pan FADGlyoxylate carboligase 4.1.1.47 0.709
3p9k SAHCaffeic acid O-methyltransferase / 0.709
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.709
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.709
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.708
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.708
5epe SAHUncharacterized protein / 0.707
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.706
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.704
4qnv GEKtRNA U34 carboxymethyltransferase / 0.704
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.702
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.700
4x3q SAHSibL / 0.699
1g1a NADdTDP-glucose 4,6-dehydratase / 0.698
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.698
3ldf SAHUncharacterized protein / 0.698
5bp7 SAHSAM-dependent methyltransferase / 0.698
3lst SAHCalO1 / 0.695
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.694
4uy6 SAHHistidine N-alpha-methyltransferase / 0.694
1x1c SAHC-20 methyltransferase / 0.693
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.693
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.691
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.691
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.691
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.690
4hh4 SAHCcbJ / 0.690
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.689
1boo SAHModification methylase PvuII 2.1.1.113 0.688
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.688
3dh0 SAMUncharacterized protein / 0.688
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.688
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.688
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.687
4rvd SAMD-mycarose 3-C-methyltransferase / 0.687
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.686
4mb2 ATPUncharacterized protein / 0.686
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.685
4b69 FADL-ornithine N(5)-monooxygenase / 0.684
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.683
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.683
1wam FADUDP-galactopyranose mutase 5.4.99.9 0.682
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.682
3ha5 SFGHydroxymycolate synthase MmaA4 2.1.1 0.682
3ou2 SAHSAM-dependent methyltransferase / 0.682
1x1b SAHC-20 methyltransferase / 0.681
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.681
4b63 FADL-ornithine N(5)-monooxygenase / 0.681
4qnu GEKtRNA U34 carboxymethyltransferase / 0.681
4xxg FADCholesterol oxidase 1.1.3.6 0.680
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.679
1y9d FADPyruvate oxidase 1.2.3.3 0.679
2gew FADCholesterol oxidase 1.1.3.6 0.679
3e23 SAMUncharacterized protein / 0.679
3ha3 SAHHydroxymycolate synthase MmaA4 2.1.1 0.679
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.679
4u2t FADCholesterol oxidase 1.1.3.6 0.679
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.679
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.678
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.678
3e8s SAHUncharacterized protein / 0.677
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.677
4dmg SAMUncharacterized protein / 0.677
4eqg A5AHistidine triad nucleotide-binding protein 1 3 0.677
4yv0 S4MSpermidine synthase, putative / 0.677
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.676
3cnj FADCholesterol oxidase 1.1.3.6 0.675
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.675
1i8t FADUDP-galactopyranose mutase 5.4.99.9 0.674
2np6 NEAModification methylase TaqI 2.1.1.72 0.674
3t7t SAHUncharacterized protein / 0.674
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.674
4kwc SAHMethyltransferase domain family / 0.674
3cox FADCholesterol oxidase 1.1.3.6 0.673
3mj4 FADUDP-galactopyranose mutase / 0.673
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.672
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.671
1uay ADNOxidoreductase / 0.671
1x1a SAMC-20 methyltransferase / 0.671
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.670
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.668
4mo2 FDAUDP-galactopyranose mutase / 0.668
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.667
1v5e FADPyruvate oxidase / 0.667
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.667
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.667
2f8l SAMLmo1582 protein / 0.666
2zfu SAHRibosomal RNA-processing protein 8 / 0.666
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.665
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.664
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.664
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.664
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.664
1cbo FADCholesterol oxidase 1.1.3.6 0.663
4fr0 SAMArsenic methyltransferase / 0.663
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.662
2ewm NAD(S)-1-Phenylethanol dehydrogenase 1.1.1.311 0.662
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.662
4hb9 FADUncharacterized protein / 0.662
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.662
4tm3 FADKtzI / 0.662
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.662
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.661
2eg5 SAH7-methylxanthosine synthase 1 / 0.661
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.660
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.660
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.659
1cc2 FADCholesterol oxidase 1.1.3.6 0.658
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.658
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.658
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.658
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.658
1u5a BIKL-lactate dehydrogenase 1.1.1.27 0.657
2plw SAMRibosomal RNA methyltransferase, putative / 0.657
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.657
3vyw SAMUncharacterized protein / 0.657
4ube 2FAAdenosine kinase 2.7.1.20 0.657
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.656
2px2 SAHGenome polyprotein 2.7.7.48 0.656
3geg NADShort-chain dehydrogenase/reductase SDR / 0.656
4poo SAMPutative RNA methylase / 0.656
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.655
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.654
5f2k SAHUncharacterized protein / 0.653
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.652
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.652
4l1x NAPAldo-keto reductase family 1 member C2 / 0.652
2zgv ADPPhosphoglycerate kinase 1 2.7.2.3 0.651
3fpf MTAUncharacterized protein / 0.651
3icp NADNAD-dependent epimerase/dehydratase / 0.651
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.651
2c4c FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.650
4yac NAIC alpha-dehydrogenase / 0.650
5f8f SFGPossible transcriptional regulatory protein / 0.650