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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
3uj8 SFG Phosphoethanolamine N-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3uj8 SFGPhosphoethanolamine N-methyltransferase / 1.082
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.994
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.985
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.979
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.928
5je2 SAHMethyl transferase / 0.852
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.841
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.815
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.800
5je3 SAHMethyl transferase / 0.797
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.795
5jdz SAHMethyl transferase / 0.794
5je4 SAHMethyl transferase / 0.782
2yqz SAMUncharacterized protein / 0.778
3lcc SAHThiocyanate methyltransferase 1 / 0.778
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.778
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.776
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.769
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.767
2gs9 SAHUncharacterized protein / 0.766
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.766
5epe SAHUncharacterized protein / 0.765
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.764
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.763
2p35 SAHTrans-aconitate 2-methyltransferase / 0.763
3t7s SAMUncharacterized protein / 0.759
3ou2 SAHSAM-dependent methyltransferase / 0.757
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.755
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.755
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.753
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.752
3e23 SAMUncharacterized protein / 0.751
3t7t SAHUncharacterized protein / 0.751
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.751
5bxy SAHPutative RNA methylase family UPF0020 / 0.751
2pan FADGlyoxylate carboligase 4.1.1.47 0.750
2qe6 SAMUncharacterized protein / 0.749
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.746
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.744
4nec SAHPutative SAM-dependent methyltransferase / 0.743
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.741
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.741
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.740
2o07 MTASpermidine synthase 2.5.1.16 0.739
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.739
3go4 SAHUncharacterized protein / 0.738
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.736
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.736
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.735
2zfu SAHRibosomal RNA-processing protein 8 / 0.735
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.735
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.733
3kkz SAMUncharacterized protein / 0.732
4hh4 SAHCcbJ / 0.730
5bp7 SAHSAM-dependent methyltransferase / 0.729
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.727
4qpp SAHProtein arginine N-methyltransferase 6 / 0.727
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.726
4yv2 S4MSpermidine synthase, putative / 0.724
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.723
4c03 SFGProtein arginine N-methyltransferase 6 / 0.723
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.722
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.721
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.720
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.720
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.715
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.715
3e9y FABAcetolactate synthase, chloroplastic 2.2.1.6 0.715
5f8f SFGPossible transcriptional regulatory protein / 0.715
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.713
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.712
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.710
4c04 SFGProtein arginine N-methyltransferase 6 / 0.709
4kwc SAHMethyltransferase domain family / 0.708
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.707
3t0i SAHPutative methyltransferase / 0.707
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.706
4gbe SAHDNA adenine methylase 2.1.1.72 0.705
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.705
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.704
3p9k SAHCaffeic acid O-methyltransferase / 0.702
2o06 MTASpermidine synthase 2.5.1.16 0.700
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.699
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.699
1g60 SAMModification methylase MboII 2.1.1.72 0.697
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.697
3bus SAHDemethylrebeccamycin-D-glucose O-methyltransferase / 0.697
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.697
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.697
1eg2 MTAModification methylase RsrI 2.1.1.72 0.696
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.696
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.695
4yac NAIC alpha-dehydrogenase / 0.695
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.694
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.694
3sxj SAMPutative methyltransferase / 0.694
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.693
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.693
3tos SAHCalS11 / 0.691
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.690
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.689
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.689
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.687
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.687
1f3l SAHProtein arginine N-methyltransferase 3 / 0.686
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.686
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.686
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.686
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.685
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.685
2xvm SAHTellurite methyltransferase 2.1.1.265 0.685
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.685
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.685
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.685
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.684
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.684
2g1p SAHDNA adenine methylase 2.1.1.72 0.683
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.683
4kvz SAHPtnL protein / 0.683
4lwp SAHArginine N-methyltransferase, putative / 0.683
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.682
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.681
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.681
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.681
4yuz S4MSpermidine synthase, putative / 0.681
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.680
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.680
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.679
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.679
3e8s SAHUncharacterized protein / 0.679
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.678
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.677
4e2x SAHMethyltransferase / 0.677
1b4v FADCholesterol oxidase 1.1.3.6 0.675
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.675
2igo FADPyranose 2-oxidase / 0.675
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.675
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.674
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.674
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.673
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.673
3rw9 DSHSpermidine synthase 2.5.1.16 0.673
4pne SAHMethyltransferase-like protein / 0.673
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.672
2rgh FADAlpha-Glycerophosphate Oxidase / 0.672
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.672
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.671
2ibt NEAModification methylase TaqI 2.1.1.72 0.670
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.669
3wv8 ATPHmd co-occurring protein HcgE / 0.669
3n1s 5GPPurine nucleoside phosphoramidase / 0.668
2eg5 SAH7-methylxanthosine synthase 1 / 0.667
2hko FADLysine-specific histone demethylase 1A 1 0.667
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.667
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.666
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.666
4qnv GEKtRNA U34 carboxymethyltransferase / 0.666
5jjr SAHGenome polyprotein / 0.666
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.664
2v7g NADUrocanate hydratase 4.2.1.49 0.664
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.664
2plw SAMRibosomal RNA methyltransferase, putative / 0.663
3ou6 SAMSAM-dependent methyltransferase / 0.663
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.662
2hms NAIKtr system potassium uptake protein A / 0.662
2px2 SAHGenome polyprotein 2.7.7.48 0.662
3lst SAHCalO1 / 0.662
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.662
4b63 FADL-ornithine N(5)-monooxygenase / 0.661
4rek FADCholesterol oxidase 1.1.3.6 0.661
4xwr FADCholesterol oxidase 1.1.3.6 0.661
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.660
2c4c FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.659
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.659
4mb2 ATPUncharacterized protein / 0.659
4rtk SAHDNA adenine methylase 2.1.1.72 0.658
2fje FADAdenylylsulfate reductase, subunit A (AprA) / 0.657
4c05 SAHProtein arginine N-methyltransferase 6 / 0.657
1y9d FADPyruvate oxidase 1.2.3.3 0.656
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.656
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.656
3rfx NADUronate dehydrogenase / 0.656
2i9k SAHModification methylase HhaI 2.1.1.37 0.655
3gyi FADCholesterol oxidase 1.1.3.6 0.655
5eku SAHArginine N-methyltransferase, putative / 0.655
2wsb NADGalactitol dehydrogenase / 0.654
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.654
3cox FADCholesterol oxidase 1.1.3.6 0.654
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.654
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.654
2z6u SAHModification methylase HhaI 2.1.1.37 0.653
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.652
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.652
4u2l SFDCholesterol oxidase 1.1.3.6 0.652
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.651
4rv9 SAHD-mycarose 3-C-methyltransferase / 0.651
1mht SAHModification methylase HhaI 2.1.1.37 0.650
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.650