Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3v97 SAH Ribosomal RNA large subunit methyltransferase K/L 2.1.1.173

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 1.172
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.839
3ldf SAHUncharacterized protein / 0.824
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.816
2qe6 SAMUncharacterized protein / 0.812
2yqz SAMUncharacterized protein / 0.808
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.804
5je2 SAHMethyl transferase / 0.789
3lcc SAHThiocyanate methyltransferase 1 / 0.785
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.778
5bxy SAHPutative RNA methylase family UPF0020 / 0.777
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.774
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.771
1yf3 SAHDNA adenine methylase / 0.769
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.765
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.762
5je3 SAHMethyl transferase / 0.762
4kvz SAHPtnL protein / 0.760
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.756
3ldg SAHUncharacterized protein / 0.753
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.750
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.749
5je4 SAHMethyl transferase / 0.746
2gs9 SAHUncharacterized protein / 0.744
4nec SAHPutative SAM-dependent methyltransferase / 0.743
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.743
4c03 SFGProtein arginine N-methyltransferase 6 / 0.742
3go4 SAHUncharacterized protein / 0.741
3mht SAHModification methylase HhaI 2.1.1.37 0.739
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.738
5bp7 SAHSAM-dependent methyltransferase / 0.738
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.736
2z6u SAHModification methylase HhaI 2.1.1.37 0.736
2yxl SFG450aa long hypothetical fmu protein / 0.735
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.735
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.732
1boo SAHModification methylase PvuII 2.1.1.113 0.731
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.731
2np7 NEAModification methylase TaqI 2.1.1.72 0.730
4kwc SAHMethyltransferase domain family / 0.728
1f3l SAHProtein arginine N-methyltransferase 3 / 0.725
2ibt NEAModification methylase TaqI 2.1.1.72 0.725
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.724
2g1p SAHDNA adenine methylase 2.1.1.72 0.723
2i9k SAHModification methylase HhaI 2.1.1.37 0.723
3ou2 SAHSAM-dependent methyltransferase / 0.722
4rtk SAHDNA adenine methylase 2.1.1.72 0.722
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.721
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.721
1ve3 SAMUncharacterized protein / 0.720
3duw SAHO-methyltransferase, putative / 0.720
2ore SAHDNA adenine methylase 2.1.1.72 0.719
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.719
5epe SAHUncharacterized protein / 0.719
1g60 SAMModification methylase MboII 2.1.1.72 0.717
2f8l SAMLmo1582 protein / 0.717
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.717
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.717
1skm SAHModification methylase HhaI 2.1.1.37 0.715
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.714
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.714
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.714
1eg2 MTAModification methylase RsrI 2.1.1.72 0.713
2uyh SAHModification methylase HhaI 2.1.1.37 0.713
2zcj SAHModification methylase HhaI 2.1.1.37 0.713
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.713
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.713
2np6 NEAModification methylase TaqI 2.1.1.72 0.712
2zfu SAHRibosomal RNA-processing protein 8 / 0.710
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.709
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.709
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.707
4c04 SFGProtein arginine N-methyltransferase 6 / 0.707
2cww SAHUncharacterized protein / 0.706
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.705
4rtj SFGDNA adenine methylase 2.1.1.72 0.704
7mht SAHModification methylase HhaI 2.1.1.37 0.704
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.703
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.703
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.702
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.702
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.702
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.702
5jdz SAHMethyl transferase / 0.702
1mht SAHModification methylase HhaI 2.1.1.37 0.700
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.700
2c7q SAHModification methylase HhaI 2.1.1.37 0.699
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.699
3rw9 DSHSpermidine synthase 2.5.1.16 0.699
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.699
4hh4 SAHCcbJ / 0.699
1nw5 SAMModification methylase RsrI 2.1.1.72 0.698
1ori SAHProtein arginine N-methyltransferase 1 / 0.698
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.698
4gbe SAHDNA adenine methylase 2.1.1.72 0.698
3tos SAHCalS11 / 0.697
3tsc NADUncharacterized protein / 0.696
10mh SAHModification methylase HhaI 2.1.1.37 0.695
3ou6 SAMSAM-dependent methyltransferase / 0.695
3t7s SAMUncharacterized protein / 0.694
1fjx SAHModification methylase HhaI 2.1.1.37 0.693
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.693
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.693
3fpf MTAUncharacterized protein / 0.692
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.692
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.691
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.691
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.690
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.689
4poo SAMPutative RNA methylase / 0.689
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.689
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.688
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.688
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.688
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.688
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.688
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.687
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.686
2o06 MTASpermidine synthase 2.5.1.16 0.686
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.686
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.686
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.686
2ih5 NEAModification methylase TaqI 2.1.1.72 0.685
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.685
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.685
4yac NAIC alpha-dehydrogenase / 0.685
1wy7 SAHUncharacterized protein / 0.684
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.684
3e8s SAHUncharacterized protein / 0.684
2p35 SAHTrans-aconitate 2-methyltransferase / 0.683
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.683
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.682
4mht SAHModification methylase HhaI 2.1.1.37 0.682
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.682
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.681
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.681
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.681
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.681
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.681
1sg9 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.680
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.680
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.680
3fri SAH16S rRNA methylase / 0.680
4dkj SAHCytosine-specific methyltransferase / 0.680
4fr0 SAMArsenic methyltransferase / 0.680
4rts SAMDNA adenine methylase 2.1.1.72 0.680
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.678
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.677
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.677
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.676
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.676
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.675
2hmv ADPKtr system potassium uptake protein A / 0.675
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.675
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.674
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.674
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.674
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.674
4lwp SAHArginine N-methyltransferase, putative / 0.674
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.673
1nw6 SFGModification methylase RsrI 2.1.1.72 0.673
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.673
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.672
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.672
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.671
4gf5 SAHCalS11 / 0.671
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.670
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.669
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.669
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.669
5bp9 SAHPutative methyltransferase protein / 0.669
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.668
2zif SAMMethyltransferase / 0.668
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.667
1g38 NEAModification methylase TaqI 2.1.1.72 0.666
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.666
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.666
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.666
1g1a NADdTDP-glucose 4,6-dehydratase / 0.665
3c3y SAHO-methyltransferase / 0.665
3qv2 SAH5-cytosine DNA methyltransferase / 0.665
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.665
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.665
2i5b ADPPyridoxine kinase / 0.664
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.663
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.662
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.662
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.662
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.661
3sxj SAMPutative methyltransferase / 0.661
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.661
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.660
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.660
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.660
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.660
3p9k SAHCaffeic acid O-methyltransferase / 0.659
4ube 2FAAdenosine kinase 2.7.1.20 0.659
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.659
2gmh FADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial 1.5.5.1 0.658
4c05 SAHProtein arginine N-methyltransferase 6 / 0.658
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.657
1y56 ATPUncharacterized protein / 0.656
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.656
3tlj SAHUncharacterized protein / 0.656
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.655
3cbg SAHO-methyltransferase / 0.654
4rtl SFGDNA adenine methylase 2.1.1.72 0.654
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.654
2xvm SAHTellurite methyltransferase 2.1.1.265 0.653
4pne SAHMethyltransferase-like protein / 0.652
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.652
3iv6 SAMUncharacterized protein / 0.651
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.650