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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
3lcv SAM 16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 1.222
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.935
3fri SAH16S rRNA methylase / 0.896
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.804
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.801
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.789
5je3 SAHMethyl transferase / 0.776
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.769
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.766
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.759
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.752
5jdz SAHMethyl transferase / 0.748
4c03 SFGProtein arginine N-methyltransferase 6 / 0.746
2yqz SAMUncharacterized protein / 0.745
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.743
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.742
2xvm SAHTellurite methyltransferase 2.1.1.265 0.741
1ve3 SAMUncharacterized protein / 0.740
3ou2 SAHSAM-dependent methyltransferase / 0.740
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.737
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.736
5je2 SAHMethyl transferase / 0.736
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.735
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.728
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.727
2zfu SAHRibosomal RNA-processing protein 8 / 0.727
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.727
5bp9 SAHPutative methyltransferase protein / 0.727
5je4 SAHMethyl transferase / 0.726
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.725
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.720
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.720
3t7t SAHUncharacterized protein / 0.719
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.717
3t7s SAMUncharacterized protein / 0.717
4c04 SFGProtein arginine N-methyltransferase 6 / 0.717
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.716
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.715
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.715
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.710
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.709
1f3l SAHProtein arginine N-methyltransferase 3 / 0.708
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.708
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.707
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.707
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.704
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.703
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.698
3lcc SAHThiocyanate methyltransferase 1 / 0.698
3lst SAHCalO1 / 0.698
4qpp SAHProtein arginine N-methyltransferase 6 / 0.698
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.697
3t0i SAHPutative methyltransferase / 0.697
3s1s SAHRestriction endonuclease BpuSI / 0.696
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.695
4pne SAHMethyltransferase-like protein / 0.694
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.693
4lwp SAHArginine N-methyltransferase, putative / 0.692
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.690
2p35 SAHTrans-aconitate 2-methyltransferase / 0.690
3tm4 SAMUncharacterized protein / 0.690
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.689
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.689
2g1p SAHDNA adenine methylase 2.1.1.72 0.688
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.688
2gs9 SAHUncharacterized protein / 0.687
3kkz SAMUncharacterized protein / 0.686
3tlj SAHUncharacterized protein / 0.685
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.685
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.684
3go4 SAHUncharacterized protein / 0.684
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.684
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.683
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.683
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.683
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.682
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.682
4rvd SAMD-mycarose 3-C-methyltransferase / 0.682
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.681
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.681
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.681
4hh4 SAHCcbJ / 0.681
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.680
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.680
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.680
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.680
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.680
5bxy SAHPutative RNA methylase family UPF0020 / 0.679
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.678
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.677
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.677
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.677
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.677
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.676
2eg5 SAH7-methylxanthosine synthase 1 / 0.676
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.674
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.674
2oyl IDCEndoglycoceramidase II / 0.674
3e23 SAMUncharacterized protein / 0.674
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.673
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.673
2ibt NEAModification methylase TaqI 2.1.1.72 0.673
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.673
3sxj SAMPutative methyltransferase / 0.673
2np7 NEAModification methylase TaqI 2.1.1.72 0.670
4rtk SAHDNA adenine methylase 2.1.1.72 0.670
4x3q SAHSibL / 0.670
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.669
3mht SAHModification methylase HhaI 2.1.1.37 0.667
3rw9 DSHSpermidine synthase 2.5.1.16 0.667
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.666
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.666
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.666
4g56 SAHProtein arginine N-methyltransferase 5 / 0.666
3ldg SAHUncharacterized protein / 0.665
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.665
5epe SAHUncharacterized protein / 0.665
3p9k SAHCaffeic acid O-methyltransferase / 0.664
3ldf SAHUncharacterized protein / 0.663
3ou6 SAMSAM-dependent methyltransferase / 0.663
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.662
1yf3 SAHDNA adenine methylase / 0.661
2ih2 NEAModification methylase TaqI 2.1.1.72 0.661
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.661
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.661
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.661
4nec SAHPutative SAM-dependent methyltransferase / 0.660
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.659
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.658
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.658
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.656
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.656
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.654
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.653
3emd SFGMethyltransferase / 0.653
4kwc SAHMethyltransferase domain family / 0.652
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.650