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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
5fa8 SAM Ribosomal protein L11 methyltransferase, putative

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 1.060
5bxy SAHPutative RNA methylase family UPF0020 / 0.927
2yqz SAMUncharacterized protein / 0.837
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.792
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.782
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.765
3go4 SAHUncharacterized protein / 0.761
5je2 SAHMethyl transferase / 0.758
5je3 SAHMethyl transferase / 0.756
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.751
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.745
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.738
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.726
4lwp SAHArginine N-methyltransferase, putative / 0.724
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.722
4hh4 SAHCcbJ / 0.718
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.717
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.714
4uy6 SAHHistidine N-alpha-methyltransferase / 0.713
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.709
4qpp SAHProtein arginine N-methyltransferase 6 / 0.709
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.707
3t7t SAHUncharacterized protein / 0.705
2p35 SAHTrans-aconitate 2-methyltransferase / 0.704
1ori SAHProtein arginine N-methyltransferase 1 / 0.703
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.703
5epe SAHUncharacterized protein / 0.698
5bp7 SAHSAM-dependent methyltransferase / 0.696
5bp9 SAHPutative methyltransferase protein / 0.696
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.695
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.694
1f3l SAHProtein arginine N-methyltransferase 3 / 0.690
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.690
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.690
2i9k SAHModification methylase HhaI 2.1.1.37 0.684
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.681
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.681
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.680
2z6u SAHModification methylase HhaI 2.1.1.37 0.677
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.677
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.677
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.677
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.677
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.676
3p9k SAHCaffeic acid O-methyltransferase / 0.676
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.676
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.675
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.675
4c04 SFGProtein arginine N-methyltransferase 6 / 0.675
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.675
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.674
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.674
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.673
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.672
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.670
4qnu GEKtRNA U34 carboxymethyltransferase / 0.669
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.669
3mht SAHModification methylase HhaI 2.1.1.37 0.668
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.668
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.667
4rtk SAHDNA adenine methylase 2.1.1.72 0.666
1orh SAHProtein arginine N-methyltransferase 1 / 0.664
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.664
4ce0 SAHProbable O-methyltransferase / 0.664
5f8f SFGPossible transcriptional regulatory protein / 0.664
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.662
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.661
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.660
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.659
3tm4 SAMUncharacterized protein / 0.659
4pgh SAMCaffeic acid O-methyltransferase / 0.659
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.657
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.657
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.657
2xvm SAHTellurite methyltransferase 2.1.1.265 0.655
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.655
5jdz SAHMethyl transferase / 0.653
4kvz SAHPtnL protein / 0.652
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.650
1wy7 SAHUncharacterized protein / 0.650
2hmv ADPKtr system potassium uptake protein A / 0.650
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.650
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.650