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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
4fp9 SAM 5-methylcytosine rRNA methyltransferase NSUN4 2.1.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 1.076
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.995
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.947
2yxl SFG450aa long hypothetical fmu protein / 0.882
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.797
4dmg SAMUncharacterized protein / 0.791
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.786
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.781
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.775
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.763
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.756
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.756
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.750
4poo SAMPutative RNA methylase / 0.750
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.745
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.744
5je4 SAHMethyl transferase / 0.744
3ldg SAHUncharacterized protein / 0.742
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.740
5je2 SAHMethyl transferase / 0.739
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.735
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.735
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.733
4rtk SAHDNA adenine methylase 2.1.1.72 0.733
2hnk SAHSAM-dependent O-methyltransferase / 0.731
2pan FADGlyoxylate carboligase 4.1.1.47 0.731
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.731
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.730
1yf3 SAHDNA adenine methylase / 0.727
4kvz SAHPtnL protein / 0.727
5je3 SAHMethyl transferase / 0.727
2o07 MTASpermidine synthase 2.5.1.16 0.726
3tos SAHCalS11 / 0.726
2np6 NEAModification methylase TaqI 2.1.1.72 0.723
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.723
4yv2 S4MSpermidine synthase, putative / 0.723
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.721
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.720
3ou2 SAHSAM-dependent methyltransferase / 0.719
1nw5 SAMModification methylase RsrI 2.1.1.72 0.718
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.717
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.716
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.714
4kwc SAHMethyltransferase domain family / 0.714
2g1p SAHDNA adenine methylase 2.1.1.72 0.709
4gbe SAHDNA adenine methylase 2.1.1.72 0.709
5jdz SAHMethyl transferase / 0.709
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.708
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.708
2np7 NEAModification methylase TaqI 2.1.1.72 0.706
3duw SAHO-methyltransferase, putative / 0.706
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.706
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.705
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.705
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.704
3ldf SAHUncharacterized protein / 0.704
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.702
3tsc NADUncharacterized protein / 0.702
1eg2 MTAModification methylase RsrI 2.1.1.72 0.701
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.700
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.700
4gf5 SAHCalS11 / 0.700
3c3y SAHO-methyltransferase / 0.698
3s55 NADPutative short-chain dehydrogenase/reductase / 0.698
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.698
1aqi SAHModification methylase TaqI 2.1.1.72 0.697
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.697
2fkn NADUrocanate hydratase 4.2.1.49 0.697
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.697
5bxy SAHPutative RNA methylase family UPF0020 / 0.697
5f2k SAHUncharacterized protein / 0.697
3cbg SAHO-methyltransferase / 0.696
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.696
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.696
2ore SAHDNA adenine methylase 2.1.1.72 0.695
3mht SAHModification methylase HhaI 2.1.1.37 0.695
1txz APRProbable ADP-ribose 1''-phosphate phosphatase YML087W 3.1.3.84 0.694
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.694
1pow FADPyruvate oxidase 1.2.3.3 0.692
2gs9 SAHUncharacterized protein / 0.692
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.691
2cww SAHUncharacterized protein / 0.690
2i9k SAHModification methylase HhaI 2.1.1.37 0.690
3fri SAH16S rRNA methylase / 0.690
5epe SAHUncharacterized protein / 0.690
2f8l SAMLmo1582 protein / 0.689
1boo SAHModification methylase PvuII 2.1.1.113 0.688
4ctk SAMGenome polyprotein / 0.688
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.687
2wsb NADGalactitol dehydrogenase / 0.686
1fjx SAHModification methylase HhaI 2.1.1.37 0.685
1ve3 SAMUncharacterized protein / 0.685
1g60 SAMModification methylase MboII 2.1.1.72 0.684
3emd SFGMethyltransferase / 0.684
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.684
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.684
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.683
1skm SAHModification methylase HhaI 2.1.1.37 0.683
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.682
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.682
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.681
2hmv ADPKtr system potassium uptake protein A / 0.679
2z6u SAHModification methylase HhaI 2.1.1.37 0.679
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.679
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.679
4rtq SAHDNA adenine methylase 2.1.1.72 0.679
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.679
5l3d FADLysine-specific histone demethylase 1A 1 0.679
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.678
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.678
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.678
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.677
4hh4 SAHCcbJ / 0.677
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.676
5f8f SFGPossible transcriptional regulatory protein / 0.676
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.676
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.675
2uyh SAHModification methylase HhaI 2.1.1.37 0.675
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.675
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.675
1x1c SAHC-20 methyltransferase / 0.673
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.673
2x2r X2OKinesin-like protein KIF11 / 0.673
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.673
4rtj SFGDNA adenine methylase 2.1.1.72 0.673
4yac NAIC alpha-dehydrogenase / 0.673
4mb2 ATPUncharacterized protein / 0.672
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.672
2zcj SAHModification methylase HhaI 2.1.1.37 0.671
3lkz SFGGenome polyprotein / 0.671
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.671
5jjr SAHGenome polyprotein / 0.671
7mht SAHModification methylase HhaI 2.1.1.37 0.671
2px2 SAHGenome polyprotein 2.7.7.48 0.669
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.669
4ft4 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.669
5bp9 SAHPutative methyltransferase protein / 0.669
1yc2 APRNAD-dependent protein deacylase 2 / 0.668
2c7q SAHModification methylase HhaI 2.1.1.37 0.667
3go4 SAHUncharacterized protein / 0.667
4c03 SFGProtein arginine N-methyltransferase 6 / 0.667
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.667
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.667
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.665
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.665
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.665
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.664
3tlj SAHUncharacterized protein / 0.664
1nfr NAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase 1.1.1.53 0.663
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.663
3s1s SAHRestriction endonuclease BpuSI / 0.663
1mht SAHModification methylase HhaI 2.1.1.37 0.662
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.662
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.662
4lwp SAHArginine N-methyltransferase, putative / 0.662
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.662
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.661
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.660
4yuz S4MSpermidine synthase, putative / 0.660
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.659
2ih2 NEAModification methylase TaqI 2.1.1.72 0.659
1mxt FAECholesterol oxidase 1.1.3.6 0.658
1n1p FADCholesterol oxidase 1.1.3.6 0.658
1n4v FADCholesterol oxidase 1.1.3.6 0.658
1n4w FADCholesterol oxidase 1.1.3.6 0.658
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.658
4xwr FADCholesterol oxidase 1.1.3.6 0.658
4xxg FADCholesterol oxidase 1.1.3.6 0.658
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.658
1b4v FADCholesterol oxidase 1.1.3.6 0.657
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.657
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.656
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.656
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.656
4tlx FDAKtzI / 0.656
2px5 SAHGenome polyprotein 2.7.7.48 0.655
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.655
2xvm SAHTellurite methyltransferase 2.1.1.265 0.654
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.654
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.653
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.653
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.653
3dh0 SAMUncharacterized protein / 0.653
4tm4 FDAKtzI / 0.653
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.652
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.652
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.652
4dkj SAHCytosine-specific methyltransferase / 0.652
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.651
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.651
5eku SAHArginine N-methyltransferase, putative / 0.651
1x1d SAHC-20 methyltransferase / 0.650
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.650