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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
4ax8 SAM O-antigen chain terminator bifunctional methyltransferase/kinase WbdD

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 1.138
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 1.050
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.774
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.773
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.747
4hh4 SAHCcbJ / 0.746
2yqz SAMUncharacterized protein / 0.744
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.740
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.739
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.736
5je2 SAHMethyl transferase / 0.731
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.722
1f3l SAHProtein arginine N-methyltransferase 3 / 0.717
4e2x SAHMethyltransferase / 0.714
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.713
3fri SAH16S rRNA methylase / 0.712
3t7s SAMUncharacterized protein / 0.708
3sxj SAMPutative methyltransferase / 0.707
3c3y SAHO-methyltransferase / 0.706
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.703
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.702
3go4 SAHUncharacterized protein / 0.700
3kkz SAMUncharacterized protein / 0.700
3t7t SAHUncharacterized protein / 0.700
3e23 SAMUncharacterized protein / 0.699
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.699
4lwp SAHArginine N-methyltransferase, putative / 0.697
4qpp SAHProtein arginine N-methyltransferase 6 / 0.697
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.696
4uy6 SAHHistidine N-alpha-methyltransferase / 0.696
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.691
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.689
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.688
5f8f SFGPossible transcriptional regulatory protein / 0.687
3t0i SAHPutative methyltransferase / 0.686
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.685
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.683
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.683
2qe6 SAMUncharacterized protein / 0.681
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.680
4fr0 SAMArsenic methyltransferase / 0.680
5jdz SAHMethyl transferase / 0.680
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.679
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.679
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.679
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.678
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.678
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.677
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.676
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.676
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.676
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.672
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.671
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.670
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.669
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.669
4kwc SAHMethyltransferase domain family / 0.669
2eg8 FOTDihydroorotase 3.5.2.3 0.668
3zzh NLGProtein ARG5,6, mitochondrial 2.7.2.8 0.668
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.668
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.667
2zfu SAHRibosomal RNA-processing protein 8 / 0.665
4qnu GEKtRNA U34 carboxymethyltransferase / 0.665
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.664
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.664
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.662
3p9k SAHCaffeic acid O-methyltransferase / 0.662
5bp7 SAHSAM-dependent methyltransferase / 0.662
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.661
4oa5 SAHO-methyltransferase family protein / 0.660
5bxy SAHPutative RNA methylase family UPF0020 / 0.660
2e82 IM3D-amino-acid oxidase 1.4.3.3 0.659
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.659
1orh SAHProtein arginine N-methyltransferase 1 / 0.658
2xvm SAHTellurite methyltransferase 2.1.1.265 0.658
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.658
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.658
3s2v 3HUGlutamate receptor ionotropic, kainate 1 / 0.658
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.656
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.654
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.653
2ayl FLPProstaglandin G/H synthase 1 1.14.99.1 0.653
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.653
4er6 AW2Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.653
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.652
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.651
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.651
1g60 SAMModification methylase MboII 2.1.1.72 0.650
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.650
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.650