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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
3b3f SAH Histone-arginine methyltransferase CARM1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3b3f SAHHistone-arginine methyltransferase CARM1 / 1.255
2y1x SAHHistone-arginine methyltransferase CARM1 / 1.167
5dxj SFGHistone-arginine methyltransferase CARM1 / 1.154
5dx8 SFGHistone-arginine methyltransferase CARM1 / 1.148
5dwq SFGHistone-arginine methyltransferase CARM1 / 1.136
2y1w SFGHistone-arginine methyltransferase CARM1 / 1.126
5dx1 SFGHistone-arginine methyltransferase CARM1 / 1.125
5dxa SFGHistone-arginine methyltransferase CARM1 / 1.100
4c03 SFGProtein arginine N-methyltransferase 6 / 1.044
2v74 SAHHistone-arginine methyltransferase CARM1 / 1.003
1f3l SAHProtein arginine N-methyltransferase 3 / 0.938
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.937
4lwp SAHArginine N-methyltransferase, putative / 0.907
4c04 SFGProtein arginine N-methyltransferase 6 / 0.905
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.882
4qpp SAHProtein arginine N-methyltransferase 6 / 0.875
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.855
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.850
5je3 SAHMethyl transferase / 0.847
5jdz SAHMethyl transferase / 0.841
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.838
5je2 SAHMethyl transferase / 0.831
2yqz SAMUncharacterized protein / 0.818
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.815
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.814
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.810
2qe6 SAMUncharacterized protein / 0.800
3go4 SAHUncharacterized protein / 0.796
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.790
4nec SAHPutative SAM-dependent methyltransferase / 0.789
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.789
3fri SAH16S rRNA methylase / 0.788
4hh4 SAHCcbJ / 0.788
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.787
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.778
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.774
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.773
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.772
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.772
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.772
3lcc SAHThiocyanate methyltransferase 1 / 0.770
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.770
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.769
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.768
5bp9 SAHPutative methyltransferase protein / 0.765
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.761
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.760
3e23 SAMUncharacterized protein / 0.759
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.759
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.757
3e8s SAHUncharacterized protein / 0.754
1ori SAHProtein arginine N-methyltransferase 1 / 0.753
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.752
4x3q SAHSibL / 0.752
3t7s SAMUncharacterized protein / 0.751
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.751
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.750
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.749
4uy6 SAHHistidine N-alpha-methyltransferase / 0.749
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.747
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.744
5bxy SAHPutative RNA methylase family UPF0020 / 0.744
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.743
2zfu SAHRibosomal RNA-processing protein 8 / 0.741
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.739
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.738
2i9k SAHModification methylase HhaI 2.1.1.37 0.737
3c3y SAHO-methyltransferase / 0.737
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.737
4rvd SAMD-mycarose 3-C-methyltransferase / 0.736
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.735
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.734
4pne SAHMethyltransferase-like protein / 0.733
5epe SAHUncharacterized protein / 0.733
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.732
2p35 SAHTrans-aconitate 2-methyltransferase / 0.726
3tm4 SAMUncharacterized protein / 0.726
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.725
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.723
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.722
5eku SAHArginine N-methyltransferase, putative / 0.722
5je4 SAHMethyl transferase / 0.722
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.721
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.721
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.720
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.720
5bp7 SAHSAM-dependent methyltransferase / 0.720
3duw SAHO-methyltransferase, putative / 0.719
4c05 SAHProtein arginine N-methyltransferase 6 / 0.719
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.719
1skm SAHModification methylase HhaI 2.1.1.37 0.718
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.718
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.717
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.717
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.716
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.716
4oa5 SAHO-methyltransferase family protein / 0.714
2ibt NEAModification methylase TaqI 2.1.1.72 0.712
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.711
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.709
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.708
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.708
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.707
4fr0 SAMArsenic methyltransferase / 0.707
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.707
2xvm SAHTellurite methyltransferase 2.1.1.265 0.706
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.706
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.706
2z6u SAHModification methylase HhaI 2.1.1.37 0.705
3lby SAHUncharacterized protein / 0.705
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.704
4kwc SAHMethyltransferase domain family / 0.704
2gs9 SAHUncharacterized protein / 0.703
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.703
3mht SAHModification methylase HhaI 2.1.1.37 0.703
4qnu GEKtRNA U34 carboxymethyltransferase / 0.703
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.702
3tos SAHCalS11 / 0.701
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.700
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.699
2ih2 NEAModification methylase TaqI 2.1.1.72 0.697
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.696
3tlj SAHUncharacterized protein / 0.696
1wy7 SAHUncharacterized protein / 0.695
7mht SAHModification methylase HhaI 2.1.1.37 0.695
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.694
2ore SAHDNA adenine methylase 2.1.1.72 0.694
3cbg SAHO-methyltransferase / 0.694
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.693
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.693
4e2x SAHMethyltransferase / 0.692
5f2k SAHUncharacterized protein / 0.692
3iv6 SAMUncharacterized protein / 0.691
3kkz SAMUncharacterized protein / 0.691
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.690
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.690
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.689
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.687
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.686
2ih5 NEAModification methylase TaqI 2.1.1.72 0.685
2np7 NEAModification methylase TaqI 2.1.1.72 0.685
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.684
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.684
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.684
3ha3 SAHHydroxymycolate synthase MmaA4 2.1.1 0.684
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.684
4rtq SAHDNA adenine methylase 2.1.1.72 0.684
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.683
1sg9 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.682
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.682
4fx9 FADCoenzyme A disulfide reductase 1.8.1.14 0.682
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.681
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.681
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.680
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.680
1nw6 SFGModification methylase RsrI 2.1.1.72 0.679
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.679
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.679
1orh SAHProtein arginine N-methyltransferase 1 / 0.678
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.676
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.676
2hnk SAHSAM-dependent O-methyltransferase / 0.675
3lst SAHCalO1 / 0.675
1x1c SAHC-20 methyltransferase / 0.674
2o06 MTASpermidine synthase 2.5.1.16 0.673
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.673
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.672
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.672
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.672
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.672
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.670
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
1yf3 SAHDNA adenine methylase / 0.669
4rtk SAHDNA adenine methylase 2.1.1.72 0.669
1boo SAHModification methylase PvuII 2.1.1.113 0.668
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.668
3ldg SAHUncharacterized protein / 0.668
5f8f SFGPossible transcriptional regulatory protein / 0.668
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.666
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.666
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.665
3oe4 610Catechol O-methyltransferase 2.1.1.6 0.665
3t0i SAHPutative methyltransferase / 0.665
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.664
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.664
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.663
1g38 NEAModification methylase TaqI 2.1.1.72 0.662
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.662
1g60 SAMModification methylase MboII 2.1.1.72 0.660
1kws UGAGalactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3 / 0.660
4rtr SAMDNA adenine methylase 2.1.1.72 0.660
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.659
1g1a NADdTDP-glucose 4,6-dehydratase / 0.659
4kvz SAHPtnL protein / 0.659
4rto SFGDNA adenine methylase 2.1.1.72 0.659
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.658
1x1d SAHC-20 methyltransferase / 0.657
3gu3 SAHMethyltransferase / 0.657
2np6 NEAModification methylase TaqI 2.1.1.72 0.656
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.655
10mh SAHModification methylase HhaI 2.1.1.37 0.653
2pan FADGlyoxylate carboligase 4.1.1.47 0.653
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.653
2g1p SAHDNA adenine methylase 2.1.1.72 0.652
2px2 SAHGenome polyprotein 2.7.7.48 0.652
3vyw SAMUncharacterized protein / 0.652
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.652
4x9n FADUncharacterized protein MG039 homolog / 0.652
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.652
2c7q SAHModification methylase HhaI 2.1.1.37 0.651
3p9k SAHCaffeic acid O-methyltransferase / 0.651
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.651
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.650