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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
2vdv SAM tRNA (guanine-N(7)-)-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 1.021
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.796
3lcc SAHThiocyanate methyltransferase 1 / 0.792
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.774
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.770
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.763
5bxy SAHPutative RNA methylase family UPF0020 / 0.762
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.757
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.756
5je4 SAHMethyl transferase / 0.751
4qpp SAHProtein arginine N-methyltransferase 6 / 0.748
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.747
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.744
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.742
3kkz SAMUncharacterized protein / 0.741
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.741
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.740
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.740
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.739
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.739
5je2 SAHMethyl transferase / 0.739
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.738
2yqz SAMUncharacterized protein / 0.736
3go4 SAHUncharacterized protein / 0.735
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.730
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.730
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.727
4c04 SFGProtein arginine N-methyltransferase 6 / 0.727
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.726
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.725
2p35 SAHTrans-aconitate 2-methyltransferase / 0.722
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.722
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.721
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.720
4hh4 SAHCcbJ / 0.720
4nec SAHPutative SAM-dependent methyltransferase / 0.720
5epe SAHUncharacterized protein / 0.719
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.718
2zfu SAHRibosomal RNA-processing protein 8 / 0.717
3fri SAH16S rRNA methylase / 0.717
3t7s SAMUncharacterized protein / 0.716
5bp7 SAHSAM-dependent methyltransferase / 0.716
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.715
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.713
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.712
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.712
3t7t SAHUncharacterized protein / 0.711
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.710
3e23 SAMUncharacterized protein / 0.708
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.707
4uy6 SAHHistidine N-alpha-methyltransferase / 0.707
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.706
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.706
2xvm SAHTellurite methyltransferase 2.1.1.265 0.705
3t0i SAHPutative methyltransferase / 0.705
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.704
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.702
4kwc SAHMethyltransferase domain family / 0.702
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.701
3iv6 SAMUncharacterized protein / 0.700
3ldg SAHUncharacterized protein / 0.699
2hnk SAHSAM-dependent O-methyltransferase / 0.698
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.698
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.698
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.697
7mht SAHModification methylase HhaI 2.1.1.37 0.697
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.696
3mht SAHModification methylase HhaI 2.1.1.37 0.696
2hmv ADPKtr system potassium uptake protein A / 0.695
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.694
4lwp SAHArginine N-methyltransferase, putative / 0.694
2qe6 SAMUncharacterized protein / 0.693
1eg2 MTAModification methylase RsrI 2.1.1.72 0.692
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.692
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.692
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.692
1f3l SAHProtein arginine N-methyltransferase 3 / 0.691
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.689
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.689
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.689
5f8f SFGPossible transcriptional regulatory protein / 0.689
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.688
2hms NAIKtr system potassium uptake protein A / 0.688
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.688
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.688
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.688
4rvd SAMD-mycarose 3-C-methyltransferase / 0.688
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.687
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.686
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.686
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.685
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.685
3gyj FADCholesterol oxidase 1.1.3.6 0.685
1ve3 SAMUncharacterized protein / 0.684
2yxl SFG450aa long hypothetical fmu protein / 0.684
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.684
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.684
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.682
4kvz SAHPtnL protein / 0.682
4x3q SAHSibL / 0.682
1orh SAHProtein arginine N-methyltransferase 1 / 0.681
2gs9 SAHUncharacterized protein / 0.681
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.681
3rw9 DSHSpermidine synthase 2.5.1.16 0.681
2ih2 NEAModification methylase TaqI 2.1.1.72 0.680
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.680
4pne SAHMethyltransferase-like protein / 0.680
1wy7 SAHUncharacterized protein / 0.679
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.679
1nw5 SAMModification methylase RsrI 2.1.1.72 0.678
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.678
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.677
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.677
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.676
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.675
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.675
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.674
4gbe SAHDNA adenine methylase 2.1.1.72 0.674
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.672
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.672
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.671
4yac NAIC alpha-dehydrogenase / 0.671
3e8s SAHUncharacterized protein / 0.670
2ore SAHDNA adenine methylase 2.1.1.72 0.669
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.669
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.668
2ih5 NEAModification methylase TaqI 2.1.1.72 0.668
3sxj SAMPutative methyltransferase / 0.668
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.667
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.667
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.666
4j34 FADKynurenine 3-monooxygenase / 0.666
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.665
4gc9 SAMDimethyladenosine transferase 1, mitochondrial 2.1.1 0.665
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.663
3c3y SAHO-methyltransferase / 0.663
3lst SAHCalO1 / 0.663
4b69 FADL-ornithine N(5)-monooxygenase / 0.663
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.662
3tm5 SFGUncharacterized protein / 0.662
4oa5 SAHO-methyltransferase family protein / 0.662
4qnu GEKtRNA U34 carboxymethyltransferase / 0.662
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.661
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.660
1ori SAHProtein arginine N-methyltransferase 1 / 0.660
2dki FAD3-hydroxybenzoate 4-monooxygenase 1.14.13.23 0.660
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.660
5bp9 SAHPutative methyltransferase protein / 0.660
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.659
1skm SAHModification methylase HhaI 2.1.1.37 0.658
3lsi FADPyranose 2-oxidase / 0.658
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.657
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.657
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.657
4mok FADPyranose 2-oxidase / 0.657
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.656
3lsm SFDPyranose 2-oxidase / 0.654
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.654
1f8s FADL-amino-acid oxidase 1.4.3.2 0.653
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.653
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.653
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.653
3p9k SAHCaffeic acid O-methyltransferase / 0.653
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.653
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.652
2z6u SAHModification methylase HhaI 2.1.1.37 0.652
3ldf SAHUncharacterized protein / 0.652
2f8l SAMLmo1582 protein / 0.651
2px2 SAHGenome polyprotein 2.7.7.48 0.651
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.651
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.650