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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
5dx1 SFG Histone-arginine methyltransferase CARM1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5dx1 SFGHistone-arginine methyltransferase CARM1 / 1.288
5dxj SFGHistone-arginine methyltransferase CARM1 / 1.279
5dx8 SFGHistone-arginine methyltransferase CARM1 / 1.259
2y1w SFGHistone-arginine methyltransferase CARM1 / 1.238
4c03 SFGProtein arginine N-methyltransferase 6 / 1.207
5dxa SFGHistone-arginine methyltransferase CARM1 / 1.205
5dwq SFGHistone-arginine methyltransferase CARM1 / 1.196
3b3f SAHHistone-arginine methyltransferase CARM1 / 1.125
2y1x SAHHistone-arginine methyltransferase CARM1 / 1.094
4c04 SFGProtein arginine N-methyltransferase 6 / 1.017
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.901
1f3l SAHProtein arginine N-methyltransferase 3 / 0.893
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.836
5je2 SAHMethyl transferase / 0.836
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.826
5jdz SAHMethyl transferase / 0.824
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.815
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.810
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.809
4qpp SAHProtein arginine N-methyltransferase 6 / 0.804
3fri SAH16S rRNA methylase / 0.802
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.801
4lwp SAHArginine N-methyltransferase, putative / 0.789
3lcc SAHThiocyanate methyltransferase 1 / 0.788
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.785
5je3 SAHMethyl transferase / 0.783
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.780
4hh4 SAHCcbJ / 0.778
5bp9 SAHPutative methyltransferase protein / 0.776
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.772
3e23 SAMUncharacterized protein / 0.769
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.765
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.762
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.759
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.746
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.743
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.743
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.742
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.741
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.739
1orh SAHProtein arginine N-methyltransferase 1 / 0.738
4pne SAHMethyltransferase-like protein / 0.738
2gs9 SAHUncharacterized protein / 0.737
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.732
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.730
2xvm SAHTellurite methyltransferase 2.1.1.265 0.729
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.729
3tm4 SAMUncharacterized protein / 0.728
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.728
4rvd SAMD-mycarose 3-C-methyltransferase / 0.727
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.725
2p35 SAHTrans-aconitate 2-methyltransferase / 0.725
3p9k SAHCaffeic acid O-methyltransferase / 0.723
2qe6 SAMUncharacterized protein / 0.722
3e8s SAHUncharacterized protein / 0.722
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.720
2i9k SAHModification methylase HhaI 2.1.1.37 0.719
3t7s SAMUncharacterized protein / 0.717
2yqz SAMUncharacterized protein / 0.713
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.713
4uy6 SAHHistidine N-alpha-methyltransferase / 0.711
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.710
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.710
4nec SAHPutative SAM-dependent methyltransferase / 0.708
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.706
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.705
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.705
2zfu SAHRibosomal RNA-processing protein 8 / 0.703
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.703
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.702
5je4 SAHMethyl transferase / 0.702
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.701
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.701
1wy7 SAHUncharacterized protein / 0.699
1skm SAHModification methylase HhaI 2.1.1.37 0.698
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.698
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.698
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.698
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.697
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.697
4oa5 SAHO-methyltransferase family protein / 0.697
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.695
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.695
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.694
2c7q SAHModification methylase HhaI 2.1.1.37 0.694
3ha5 SFGHydroxymycolate synthase MmaA4 2.1.1 0.694
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.693
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.692
2ibt NEAModification methylase TaqI 2.1.1.72 0.691
3iv6 SAMUncharacterized protein / 0.691
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.691
2ore SAHDNA adenine methylase 2.1.1.72 0.690
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.690
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.690
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.689
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.687
2f8l SAMLmo1582 protein / 0.686
3cbg SAHO-methyltransferase / 0.685
4yac NAIC alpha-dehydrogenase / 0.685
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.684
2np7 NEAModification methylase TaqI 2.1.1.72 0.684
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.684
3ou2 SAHSAM-dependent methyltransferase / 0.684
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.684
5bxy SAHPutative RNA methylase family UPF0020 / 0.684
5epe SAHUncharacterized protein / 0.684
3lst SAHCalO1 / 0.683
5f2k SAHUncharacterized protein / 0.683
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.682
1yf3 SAHDNA adenine methylase / 0.682
5eku SAHArginine N-methyltransferase, putative / 0.682
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.681
3c3y SAHO-methyltransferase / 0.681
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.680
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.680
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.679
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.679
4qnu GEKtRNA U34 carboxymethyltransferase / 0.679
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.678
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.676
7mht SAHModification methylase HhaI 2.1.1.37 0.676
3ha3 SAHHydroxymycolate synthase MmaA4 2.1.1 0.675
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.674
3kpf FADPolyamine oxidase 1.5.3.14 0.674
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.674
1mxt FAECholesterol oxidase 1.1.3.6 0.673
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.673
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.673
1boo SAHModification methylase PvuII 2.1.1.113 0.672
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.672
1b4v FADCholesterol oxidase 1.1.3.6 0.671
2ih5 NEAModification methylase TaqI 2.1.1.72 0.670
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.670
4rtq SAHDNA adenine methylase 2.1.1.72 0.670
3tr6 SAHO-methyltransferase / 0.669
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.669
1h81 FADPolyamine oxidase 1.5.3.14 0.668
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.668
4kwc SAHMethyltransferase domain family / 0.668
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.667
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.665
5bp7 SAHSAM-dependent methyltransferase / 0.664
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.664
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.663
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.663
2yxl SFG450aa long hypothetical fmu protein / 0.663
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.663
1x1a SAMC-20 methyltransferase / 0.662
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.662
3bwc SAMSpermidine synthase, putative / 0.662
4c05 SAHProtein arginine N-methyltransferase 6 / 0.662
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.660
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.660
3daf FEG5,10-methenyltetrahydromethanopterin hydrogenase 1.12.98.2 0.660
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.660
4rtk SAHDNA adenine methylase 2.1.1.72 0.660
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.659
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.659
4kvz SAHPtnL protein / 0.659
3lby SAHUncharacterized protein / 0.658
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.658
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.658
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.657
2p0a ANPSynapsin-3 / 0.657
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.656
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.656
1ori SAHProtein arginine N-methyltransferase 1 / 0.655
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.655
4e2x SAHMethyltransferase / 0.655
2g1p SAHDNA adenine methylase 2.1.1.72 0.654
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.654
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.654
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.653
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.653
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.653
4rtr SAMDNA adenine methylase 2.1.1.72 0.653
1g60 SAMModification methylase MboII 2.1.1.72 0.652
3gu3 SAHMethyltransferase / 0.652
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.652
3dag FEG5,10-methenyltetrahydromethanopterin hydrogenase 1.12.98.2 0.651
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.651
3eld SFGMethyltransferase / 0.650
4rtj SFGDNA adenine methylase 2.1.1.72 0.650