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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
2bzg SAH Thiopurine S-methyltransferase 2.1.1.67

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 1.167
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.959
3lcc SAHThiocyanate methyltransferase 1 / 0.834
1f3l SAHProtein arginine N-methyltransferase 3 / 0.827
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.816
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.814
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.810
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.809
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.807
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.806
3go4 SAHUncharacterized protein / 0.798
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.796
3t7s SAMUncharacterized protein / 0.796
5je3 SAHMethyl transferase / 0.791
4c03 SFGProtein arginine N-methyltransferase 6 / 0.790
4nec SAHPutative SAM-dependent methyltransferase / 0.786
4rtk SAHDNA adenine methylase 2.1.1.72 0.786
2qe6 SAMUncharacterized protein / 0.782
5jdz SAHMethyl transferase / 0.781
4lwp SAHArginine N-methyltransferase, putative / 0.778
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.778
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.778
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.777
1yf3 SAHDNA adenine methylase / 0.775
4gbe SAHDNA adenine methylase 2.1.1.72 0.773
5je2 SAHMethyl transferase / 0.773
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.772
3e8s SAHUncharacterized protein / 0.771
5bp9 SAHPutative methyltransferase protein / 0.770
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.769
4qpp SAHProtein arginine N-methyltransferase 6 / 0.767
1g60 SAMModification methylase MboII 2.1.1.72 0.765
3fri SAH16S rRNA methylase / 0.765
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.763
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.762
3ou2 SAHSAM-dependent methyltransferase / 0.762
2ore SAHDNA adenine methylase 2.1.1.72 0.760
5je4 SAHMethyl transferase / 0.760
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.758
2g1p SAHDNA adenine methylase 2.1.1.72 0.757
2gs9 SAHUncharacterized protein / 0.755
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.755
3ldf SAHUncharacterized protein / 0.755
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.755
4rtj SFGDNA adenine methylase 2.1.1.72 0.755
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.754
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.753
4x3q SAHSibL / 0.753
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.751
5bp7 SAHSAM-dependent methyltransferase / 0.747
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.746
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.743
1eg2 MTAModification methylase RsrI 2.1.1.72 0.742
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.742
5bxy SAHPutative RNA methylase family UPF0020 / 0.742
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.741
3mht SAHModification methylase HhaI 2.1.1.37 0.740
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.740
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.737
1boo SAHModification methylase PvuII 2.1.1.113 0.736
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.736
1y9d FADPyruvate oxidase 1.2.3.3 0.735
2yqz SAMUncharacterized protein / 0.734
4wec NADShort chain dehydrogenase / 0.734
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.732
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.731
4rtr SAMDNA adenine methylase 2.1.1.72 0.730
4uy6 SAHHistidine N-alpha-methyltransferase / 0.729
2ibt NEAModification methylase TaqI 2.1.1.72 0.728
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.728
2ih2 NEAModification methylase TaqI 2.1.1.72 0.727
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.727
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.726
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.726
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.725
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.725
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.723
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.723
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.721
4yac NAIC alpha-dehydrogenase / 0.721
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.720
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.719
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.718
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.718
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.717
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.716
4rts SAMDNA adenine methylase 2.1.1.72 0.716
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.716
2zfu SAHRibosomal RNA-processing protein 8 / 0.715
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.715
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.715
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.715
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.715
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.715
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.714
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.714
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.712
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.712
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.711
3c3y SAHO-methyltransferase / 0.711
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.711
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.711
2ih5 NEAModification methylase TaqI 2.1.1.72 0.710
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.709
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.709
4hh4 SAHCcbJ / 0.708
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.708
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.707
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.707
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.705
2o06 MTASpermidine synthase 2.5.1.16 0.705
4fr0 SAMArsenic methyltransferase / 0.705
1nw6 SFGModification methylase RsrI 2.1.1.72 0.704
2z6u SAHModification methylase HhaI 2.1.1.37 0.703
3e23 SAMUncharacterized protein / 0.701
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.701
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.700
2i9k SAHModification methylase HhaI 2.1.1.37 0.700
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.700
4fn4 NADShort chain dehydrogenase / 0.700
2o07 MTASpermidine synthase 2.5.1.16 0.699
2uyh SAHModification methylase HhaI 2.1.1.37 0.699
5f8f SFGPossible transcriptional regulatory protein / 0.699
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.698
5cku FADL-ornithine N(5)-monooxygenase / 0.697
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.696
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.695
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.694
3p9k SAHCaffeic acid O-methyltransferase / 0.694
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.693
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.693
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.692
1nw5 SAMModification methylase RsrI 2.1.1.72 0.692
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.692
1nc1 MTH5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase 3.2.2.9 0.690
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.690
10mh SAHModification methylase HhaI 2.1.1.37 0.689
2c7q SAHModification methylase HhaI 2.1.1.37 0.689
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.689
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.689
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.689
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.689
3iv6 SAMUncharacterized protein / 0.689
7mht SAHModification methylase HhaI 2.1.1.37 0.689
2zcj SAHModification methylase HhaI 2.1.1.37 0.688
1skm SAHModification methylase HhaI 2.1.1.37 0.687
3fpf MTAUncharacterized protein / 0.686
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.686
4qnv GEKtRNA U34 carboxymethyltransferase / 0.686
1g38 NEAModification methylase TaqI 2.1.1.72 0.685
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.685
4poo SAMPutative RNA methylase / 0.685
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.684
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.684
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.684
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.683
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.683
3i9j NFDADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 3.2.2.6 0.682
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.681
4kwc SAHMethyltransferase domain family / 0.680
2px5 SAHGenome polyprotein 2.7.7.48 0.679
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.679
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.679
4dkj SAHCytosine-specific methyltransferase / 0.679
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.679
2hmv ADPKtr system potassium uptake protein A / 0.678
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.678
4rvd SAMD-mycarose 3-C-methyltransferase / 0.678
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.677
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.676
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.676
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.675
3dzi RGTADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 3.2.2.6 0.675
3ldg SAHUncharacterized protein / 0.675
4eqg A5AHistidine triad nucleotide-binding protein 1 3 0.675
1sg9 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.674
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.674
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.674
4h0n SAHDnmt2 / 0.674
3tos SAHCalS11 / 0.673
4d79 ATPtRNA threonylcarbamoyladenosine dehydratase 6.1 0.672
4eqe KAAHistidine triad nucleotide-binding protein 1 3 0.672
4gol SA8DNA adenine methylase 2.1.1.72 0.672
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.671
4gf5 SAHCalS11 / 0.671
4rtn SAHDNA adenine methylase 2.1.1.72 0.671
4kvz SAHPtnL protein / 0.669
1nm5 NAPNAD(P) transhydrogenase subunit beta 1.6.1.2 0.667
1pow FADPyruvate oxidase 1.2.3.3 0.667
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.667
3kkz SAMUncharacterized protein / 0.667
4yuz S4MSpermidine synthase, putative / 0.666
5d7p AR6NAD-dependent protein deacetylase sirtuin-2 3.5.1 0.666
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.666
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.665
2z86 UGAChondroitin synthase 2.4.1.175 0.665
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.665
4c04 SFGProtein arginine N-methyltransferase 6 / 0.665
4g67 SAHUncharacterized ACR, COG1565 superfamily / 0.665
4rtp SAMDNA adenine methylase 2.1.1.72 0.665
5mht SAHModification methylase HhaI 2.1.1.37 0.665
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.664
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.664
4qnu GEKtRNA U34 carboxymethyltransferase / 0.664
5f2k SAHUncharacterized protein / 0.664
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.663
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.663
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.663
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.663
1ori SAHProtein arginine N-methyltransferase 1 / 0.662
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.662
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.662
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.662
2cww SAHUncharacterized protein / 0.661
2i0z FADNAD(FAD)-utilizing dehydrogenases / 0.661
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.661
4rtm SAMDNA adenine methylase 2.1.1.72 0.661
1aqi SAHModification methylase TaqI 2.1.1.72 0.660
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.660
4mb2 ATPUncharacterized protein / 0.660
3eey SAMrRNA methylase / 0.659
1x1a SAMC-20 methyltransferase / 0.658
1x1c SAHC-20 methyltransferase / 0.658
4c05 SAHProtein arginine N-methyltransferase 6 / 0.658
1ve3 SAMUncharacterized protein / 0.657
3n1s 5GPPurine nucleoside phosphoramidase / 0.657
5d4u SAMUncharacterized protein MJ0489 / 0.656
1wy7 SAHUncharacterized protein / 0.655
3cbg SAHO-methyltransferase / 0.655
3emd SFGMethyltransferase / 0.655
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.655
1v59 NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.654
3ou7 SAMSAM-dependent methyltransferase / 0.654
4bmz MTAAminodeoxyfutalosine nucleosidase / 0.654
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.653
3uov FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.653
3uq9 TBNPutative adenosine kinase / 0.653
4e2x SAHMethyltransferase / 0.653
1xqp 8HGN-glycosylase/DNA lyase / 0.652
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.652
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.652
4f86 SFGGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.652
5epe SAHUncharacterized protein / 0.652
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.651
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.651
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.651
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.651
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.651
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.650
2bm9 SAMCephalosporin hydroxylase CmcI / 0.650
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.650