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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
5dxj SFG Histone-arginine methyltransferase CARM1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5dxj SFGHistone-arginine methyltransferase CARM1 / 1.308
5dx8 SFGHistone-arginine methyltransferase CARM1 / 1.283
5dx1 SFGHistone-arginine methyltransferase CARM1 / 1.279
5dxa SFGHistone-arginine methyltransferase CARM1 / 1.245
2y1w SFGHistone-arginine methyltransferase CARM1 / 1.223
4c03 SFGProtein arginine N-methyltransferase 6 / 1.192
5dwq SFGHistone-arginine methyltransferase CARM1 / 1.182
3b3f SAHHistone-arginine methyltransferase CARM1 / 1.154
2y1x SAHHistone-arginine methyltransferase CARM1 / 1.147
4c04 SFGProtein arginine N-methyltransferase 6 / 0.954
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.939
5je2 SAHMethyl transferase / 0.889
1f3l SAHProtein arginine N-methyltransferase 3 / 0.887
4hh4 SAHCcbJ / 0.844
3lcc SAHThiocyanate methyltransferase 1 / 0.835
4qpp SAHProtein arginine N-methyltransferase 6 / 0.813
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.805
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.804
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.803
3fri SAH16S rRNA methylase / 0.802
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.798
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.794
2yqz SAMUncharacterized protein / 0.790
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.789
4lwp SAHArginine N-methyltransferase, putative / 0.789
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.786
3e8s SAHUncharacterized protein / 0.786
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.785
4nec SAHPutative SAM-dependent methyltransferase / 0.784
5je3 SAHMethyl transferase / 0.780
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.779
3kkz SAMUncharacterized protein / 0.778
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.776
5jdz SAHMethyl transferase / 0.773
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.771
4e2x SAHMethyltransferase / 0.770
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.770
3ou2 SAHSAM-dependent methyltransferase / 0.767
5bp9 SAHPutative methyltransferase protein / 0.760
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.758
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.757
4uy6 SAHHistidine N-alpha-methyltransferase / 0.757
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.756
3iv6 SAMUncharacterized protein / 0.756
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.754
5f8f SFGPossible transcriptional regulatory protein / 0.753
3go4 SAHUncharacterized protein / 0.752
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.751
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.750
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.750
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.748
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.747
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.746
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.745
1orh SAHProtein arginine N-methyltransferase 1 / 0.744
3e23 SAMUncharacterized protein / 0.744
2xvm SAHTellurite methyltransferase 2.1.1.265 0.742
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.741
3sxj SAMPutative methyltransferase / 0.741
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.741
2gs9 SAHUncharacterized protein / 0.734
5je4 SAHMethyl transferase / 0.734
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.730
4rvd SAMD-mycarose 3-C-methyltransferase / 0.729
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.727
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.722
4x3q SAHSibL / 0.721
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.719
4oa5 SAHO-methyltransferase family protein / 0.719
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.718
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.717
3t7s SAMUncharacterized protein / 0.717
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.717
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.715
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.715
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.714
4fr0 SAMArsenic methyltransferase / 0.714
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.713
4pne SAHMethyltransferase-like protein / 0.713
1h81 FADPolyamine oxidase 1.5.3.14 0.712
2qe6 SAMUncharacterized protein / 0.711
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.711
3tm4 SAMUncharacterized protein / 0.711
2hnk SAHSAM-dependent O-methyltransferase / 0.709
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.709
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.708
5epe SAHUncharacterized protein / 0.708
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.707
3p9k SAHCaffeic acid O-methyltransferase / 0.707
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.706
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.705
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.705
1ori SAHProtein arginine N-methyltransferase 1 / 0.704
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.702
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.701
1wy7 SAHUncharacterized protein / 0.701
1yf3 SAHDNA adenine methylase / 0.700
4qnu GEKtRNA U34 carboxymethyltransferase / 0.700
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.698
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.697
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.697
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.696
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.696
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.695
3cbg SAHO-methyltransferase / 0.694
3tm5 SFGUncharacterized protein / 0.694
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.694
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.694
2i9k SAHModification methylase HhaI 2.1.1.37 0.693
3ha5 SFGHydroxymycolate synthase MmaA4 2.1.1 0.693
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.693
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.692
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.692
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.690
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.690
4rtk SAHDNA adenine methylase 2.1.1.72 0.690
5eku SAHArginine N-methyltransferase, putative / 0.690
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.689
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.689
3c3y SAHO-methyltransferase / 0.689
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.689
4c05 SAHProtein arginine N-methyltransferase 6 / 0.688
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.688
2c7q SAHModification methylase HhaI 2.1.1.37 0.687
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.686
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.686
2zfu SAHRibosomal RNA-processing protein 8 / 0.685
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.685
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.685
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.684
5bxy SAHPutative RNA methylase family UPF0020 / 0.684
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.682
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.682
2ih2 NEAModification methylase TaqI 2.1.1.72 0.681
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.681
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.680
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.679
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.679
4kwc SAHMethyltransferase domain family / 0.679
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.677
4udq FAD5-(hydroxymethyl)furfural oxidase / 0.676
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.675
7mht SAHModification methylase HhaI 2.1.1.37 0.674
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.673
2ibt NEAModification methylase TaqI 2.1.1.72 0.673
2pkm ADNAdenosine kinase 2.7.1.20 0.672
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.672
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.672
2z6u SAHModification methylase HhaI 2.1.1.37 0.671
4rtr SAMDNA adenine methylase 2.1.1.72 0.671
3lst SAHCalO1 / 0.670
4rtq SAHDNA adenine methylase 2.1.1.72 0.669
2f8l SAMLmo1582 protein / 0.668
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.668
1g60 SAMModification methylase MboII 2.1.1.72 0.667
4dmg SAMUncharacterized protein / 0.667
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.666
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.665
2ore SAHDNA adenine methylase 2.1.1.72 0.664
2p35 SAHTrans-aconitate 2-methyltransferase / 0.664
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.664
1boo SAHModification methylase PvuII 2.1.1.113 0.663
2ih5 NEAModification methylase TaqI 2.1.1.72 0.663
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.663
4qnv GEKtRNA U34 carboxymethyltransferase / 0.663
2plw SAMRibosomal RNA methyltransferase, putative / 0.662
2yxl SFG450aa long hypothetical fmu protein / 0.662
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.662
1g38 NEAModification methylase TaqI 2.1.1.72 0.661
2px2 SAHGenome polyprotein 2.7.7.48 0.661
1txz APRProbable ADP-ribose 1''-phosphate phosphatase YML087W 3.1.3.84 0.660
3gu3 SAHMethyltransferase / 0.660
5bp7 SAHSAM-dependent methyltransferase / 0.660
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.659
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.658
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.658
1cq6 PY4Aspartate aminotransferase 2.6.1.1 0.657
2g1p SAHDNA adenine methylase 2.1.1.72 0.657
3tr6 SAHO-methyltransferase / 0.657
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.657
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.656
3tlj SAHUncharacterized protein / 0.656
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.656
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.656
1x1d SAHC-20 methyltransferase / 0.655
3lby SAHUncharacterized protein / 0.655
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.654
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.654
4fx9 FADCoenzyme A disulfide reductase 1.8.1.14 0.653
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.652
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.651
3bwc SAMSpermidine synthase, putative / 0.651
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.651
4kvz SAHPtnL protein / 0.650