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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
3t7t SAH Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3t7t SAHUncharacterized protein / 1.024
3t7s SAMUncharacterized protein / 0.863
3t0i SAHPutative methyltransferase / 0.842
3kkz SAMUncharacterized protein / 0.825
3sxj SAMPutative methyltransferase / 0.812
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.785
4nec SAHPutative SAM-dependent methyltransferase / 0.770
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.770
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.766
2yqz SAMUncharacterized protein / 0.761
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.761
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.759
4hh4 SAHCcbJ / 0.752
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.751
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.750
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.750
5je2 SAHMethyl transferase / 0.750
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.743
5jdz SAHMethyl transferase / 0.742
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.740
4c03 SFGProtein arginine N-methyltransferase 6 / 0.736
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.730
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.730
3lst SAHCalO1 / 0.729
3lcc SAHThiocyanate methyltransferase 1 / 0.725
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.724
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.719
5bp9 SAHPutative methyltransferase protein / 0.719
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.717
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.716
3ou2 SAHSAM-dependent methyltransferase / 0.714
4kvz SAHPtnL protein / 0.714
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.714
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.711
2xvm SAHTellurite methyltransferase 2.1.1.265 0.711
2zfu SAHRibosomal RNA-processing protein 8 / 0.711
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.708
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.705
2gs9 SAHUncharacterized protein / 0.702
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.702
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.700
3p9k SAHCaffeic acid O-methyltransferase / 0.698
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.697
2qe6 SAMUncharacterized protein / 0.696
3go4 SAHUncharacterized protein / 0.695
4uy6 SAHHistidine N-alpha-methyltransferase / 0.695
5je4 SAHMethyl transferase / 0.695
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.693
3fri SAH16S rRNA methylase / 0.693
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.693
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.692
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.691
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.690
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.689
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.688
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.686
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.685
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.685
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.685
5bxy SAHPutative RNA methylase family UPF0020 / 0.680
1ve3 SAMUncharacterized protein / 0.679
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.677
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.677
4kwc SAHMethyltransferase domain family / 0.677
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.676
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.675
5je3 SAHMethyl transferase / 0.674
2p35 SAHTrans-aconitate 2-methyltransferase / 0.673
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.673
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.672
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.671
4qpp SAHProtein arginine N-methyltransferase 6 / 0.671
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.669
1vso AT1Glutamate receptor ionotropic, kainate 1 / 0.667
1orh SAHProtein arginine N-methyltransferase 1 / 0.665
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.665
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.663
4x3q SAHSibL / 0.663
2i9k SAHModification methylase HhaI 2.1.1.37 0.662
3c36 KAIGlutamate receptor ionotropic, kainate 1 / 0.661
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.660
3mht SAHModification methylase HhaI 2.1.1.37 0.660
5f8f SFGPossible transcriptional regulatory protein / 0.660
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.659
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.659
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.659
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.656
4qnu GEKtRNA U34 carboxymethyltransferase / 0.656
3cbg SAHO-methyltransferase / 0.655
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.655
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.654
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.653
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.652
3zku HCVIsopenicillin N synthase 1.21.3.1 0.652
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.652
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.650