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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
4r6x SAH Phosphoethanolamine N-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.990
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.876
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.859
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.841
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.841
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.795
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.790
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.783
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.775
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.770
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.766
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.761
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.756
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.751
4pne SAHMethyltransferase-like protein / 0.748
4hh4 SAHCcbJ / 0.744
4kvz SAHPtnL protein / 0.739
5je2 SAHMethyl transferase / 0.739
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.737
2zfu SAHRibosomal RNA-processing protein 8 / 0.737
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.728
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.727
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.726
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.726
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.723
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.721
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.721
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.720
2qe6 SAMUncharacterized protein / 0.719
5epe SAHUncharacterized protein / 0.719
3ou2 SAHSAM-dependent methyltransferase / 0.713
5f2k SAHUncharacterized protein / 0.713
4f86 SFGGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.711
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.711
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.710
3e23 SAMUncharacterized protein / 0.709
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.709
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.708
4qpp SAHProtein arginine N-methyltransferase 6 / 0.705
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.705
3kkz SAMUncharacterized protein / 0.703
4c03 SFGProtein arginine N-methyltransferase 6 / 0.703
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.703
5bp7 SAHSAM-dependent methyltransferase / 0.702
7mht SAHModification methylase HhaI 2.1.1.37 0.702
2gs9 SAHUncharacterized protein / 0.700
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.698
4c05 SAHProtein arginine N-methyltransferase 6 / 0.696
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.696
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.694
3e8s SAHUncharacterized protein / 0.694
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.694
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.693
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.693
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.693
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.692
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.692
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.692
1f3l SAHProtein arginine N-methyltransferase 3 / 0.691
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.691
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.691
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.690
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.687
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.685
3rw9 DSHSpermidine synthase 2.5.1.16 0.684
4lwp SAHArginine N-methyltransferase, putative / 0.684
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.683
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.683
3lcc SAHThiocyanate methyltransferase 1 / 0.682
4rtk SAHDNA adenine methylase 2.1.1.72 0.682
5jdz SAHMethyl transferase / 0.682
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.681
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.680
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.679
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.678
2c7q SAHModification methylase HhaI 2.1.1.37 0.678
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.678
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.678
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.677
3bwc SAMSpermidine synthase, putative / 0.674
3he3 FADUDP-galactopyranose mutase / 0.674
4ww4 ADPRuvB-like helicase / 0.674
4yac NAIC alpha-dehydrogenase / 0.674
3fri SAH16S rRNA methylase / 0.673
3t0i SAHPutative methyltransferase / 0.673
3t7s SAMUncharacterized protein / 0.673
2eg5 SAH7-methylxanthosine synthase 1 / 0.672
4kwc SAHMethyltransferase domain family / 0.672
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.671
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.670
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.670
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.669
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.668
4c04 SFGProtein arginine N-methyltransferase 6 / 0.668
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.668
3iv6 SAMUncharacterized protein / 0.667
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.666
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.666
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.665
3t7t SAHUncharacterized protein / 0.665
2z6u SAHModification methylase HhaI 2.1.1.37 0.664
3c3y SAHO-methyltransferase / 0.663
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.662
9mht SAHModification methylase HhaI 2.1.1.37 0.662
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.661
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.661
1fjx SAHModification methylase HhaI 2.1.1.37 0.660
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.660
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.660
3tlj SAHUncharacterized protein / 0.659
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.659
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.658
2ih5 NEAModification methylase TaqI 2.1.1.72 0.658
2xe8 ACPPhosphoglycerate kinase 1 2.7.2.3 0.658
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.658
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.658
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.658
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.657
3bg7 FADPyranose 2-oxidase / 0.657
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.656
1boo SAHModification methylase PvuII 2.1.1.113 0.655
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.655
3mht SAHModification methylase HhaI 2.1.1.37 0.655
3uk6 ADPRuvB-like 2 3.6.4.12 0.655
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.655
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.654
3k4c FADPyranose 2-oxidase / 0.654
1b38 ATPCyclin-dependent kinase 2 2.7.11.22 0.652
1yf3 SAHDNA adenine methylase / 0.652
3lct ADPALK tyrosine kinase receptor 2.7.10.1 0.652
3ldg SAHUncharacterized protein / 0.652
3qv2 SAH5-cytosine DNA methyltransferase / 0.652
3tos SAHCalS11 / 0.652
10mh SAHModification methylase HhaI 2.1.1.37 0.651
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.651
4qnv GEKtRNA U34 carboxymethyltransferase / 0.651
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.651
4nec SAHPutative SAM-dependent methyltransferase / 0.650
4qa2 SHHHistone deacetylase 8 3.5.1.98 0.650