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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
1qao SAM rRNA adenine N-6-methyltransferase 2.1.1.184

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 1.038
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.874
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.839
3ou2 SAHSAM-dependent methyltransferase / 0.777
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.762
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.760
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.752
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.740
4c03 SFGProtein arginine N-methyltransferase 6 / 0.740
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.738
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.734
2g1p SAHDNA adenine methylase 2.1.1.72 0.732
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.732
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.730
2i9k SAHModification methylase HhaI 2.1.1.37 0.724
2o06 MTASpermidine synthase 2.5.1.16 0.713
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.712
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.710
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.708
3ldg SAHUncharacterized protein / 0.707
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.706
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.705
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.705
2p35 SAHTrans-aconitate 2-methyltransferase / 0.703
3tm4 SAMUncharacterized protein / 0.703
2xvm SAHTellurite methyltransferase 2.1.1.265 0.702
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.702
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.701
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.700
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.700
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.700
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.699
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.699
2zif SAMMethyltransferase / 0.698
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.698
3go4 SAHUncharacterized protein / 0.697
4rtk SAHDNA adenine methylase 2.1.1.72 0.697
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.694
3ua3 SAHProtein arginine N-methyltransferase 5 / 0.693
1wy7 SAHUncharacterized protein / 0.690
2gs9 SAHUncharacterized protein / 0.690
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.689
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.689
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.688
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.688
2hms NAIKtr system potassium uptake protein A / 0.687
4yv2 S4MSpermidine synthase, putative / 0.687
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.686
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.686
4kwc SAHMethyltransferase domain family / 0.686
3lcc SAHThiocyanate methyltransferase 1 / 0.685
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.685
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.684
1f3l SAHProtein arginine N-methyltransferase 3 / 0.683
4dmg SAMUncharacterized protein / 0.683
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.682
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.681
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.681
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.680
4qpp SAHProtein arginine N-methyltransferase 6 / 0.680
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.679
4yac NAIC alpha-dehydrogenase / 0.679
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.677
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.676
3mht SAHModification methylase HhaI 2.1.1.37 0.676
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.676
4lwp SAHArginine N-methyltransferase, putative / 0.676
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.675
3rw9 DSHSpermidine synthase 2.5.1.16 0.675
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.675
4nec SAHPutative SAM-dependent methyltransferase / 0.675
2hnk SAHSAM-dependent O-methyltransferase / 0.674
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.672
2yqz SAMUncharacterized protein / 0.672
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.672
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.672
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.671
2ibt NEAModification methylase TaqI 2.1.1.72 0.671
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.670
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.670
1g38 NEAModification methylase TaqI 2.1.1.72 0.669
2c7q SAHModification methylase HhaI 2.1.1.37 0.669
2zcj SAHModification methylase HhaI 2.1.1.37 0.669
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.669
4rtq SAHDNA adenine methylase 2.1.1.72 0.669
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.668
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.668
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.667
2z6u SAHModification methylase HhaI 2.1.1.37 0.667
3bus SAHDemethylrebeccamycin-D-glucose O-methyltransferase / 0.667
2xe8 ACPPhosphoglycerate kinase 1 2.7.2.3 0.666
4c04 SFGProtein arginine N-methyltransferase 6 / 0.666
2ih2 NEAModification methylase TaqI 2.1.1.72 0.665
4gf5 SAHCalS11 / 0.665
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.664
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.664
3bwc SAMSpermidine synthase, putative / 0.664
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.662
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.662
2px2 SAHGenome polyprotein 2.7.7.48 0.662
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.662
1s7g APRNAD-dependent protein deacylase 2 / 0.661
2ore SAHDNA adenine methylase 2.1.1.72 0.661
4hh4 SAHCcbJ / 0.661
1skm SAHModification methylase HhaI 2.1.1.37 0.660
3fpf MTAUncharacterized protein / 0.660
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.660
1n4u FAECholesterol oxidase 1.1.3.6 0.659
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.659
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.659
3abi NADUncharacterized protein / 0.659
1mxt FAECholesterol oxidase 1.1.3.6 0.658
1n4v FADCholesterol oxidase 1.1.3.6 0.658
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.658
3cnj FADCholesterol oxidase 1.1.3.6 0.658
3gyj FADCholesterol oxidase 1.1.3.6 0.658
4u2s FDACholesterol oxidase 1.1.3.6 0.658
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.657
2yxl SFG450aa long hypothetical fmu protein / 0.657
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.657
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.656
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.656
3oe4 610Catechol O-methyltransferase 2.1.1.6 0.655
3p9c SAHCaffeic acid O-methyltransferase / 0.655
5eku SAHArginine N-methyltransferase, putative / 0.655
2f8l SAMLmo1582 protein / 0.654
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.654
5epe SAHUncharacterized protein / 0.654
1x1c SAHC-20 methyltransferase / 0.653
2fkn NADUrocanate hydratase 4.2.1.49 0.653
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.653
2c4c FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.652
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.652
4ctk SAMGenome polyprotein / 0.652
1ori SAHProtein arginine N-methyltransferase 1 / 0.651
1x1b SAHC-20 methyltransferase / 0.651
2uyh SAHModification methylase HhaI 2.1.1.37 0.651
4pgh SAMCaffeic acid O-methyltransferase / 0.651
1ve3 SAMUncharacterized protein / 0.650
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.650
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.650