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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
4fzv 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
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 1.100
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.995
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.984
2yxl SFG450aa long hypothetical fmu protein / 0.889
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.830
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.806
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.801
1yf3 SAHDNA adenine methylase / 0.778
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.778
1boo SAHModification methylase PvuII 2.1.1.113 0.771
5jdz SAHMethyl transferase / 0.767
5je3 SAHMethyl transferase / 0.767
4dmg SAMUncharacterized protein / 0.765
5je2 SAHMethyl transferase / 0.764
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.762
4poo SAMPutative RNA methylase / 0.762
4rtk SAHDNA adenine methylase 2.1.1.72 0.761
2ore SAHDNA adenine methylase 2.1.1.72 0.758
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.758
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.756
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.755
4gbe SAHDNA adenine methylase 2.1.1.72 0.753
2g1p SAHDNA adenine methylase 2.1.1.72 0.751
4rtj SFGDNA adenine methylase 2.1.1.72 0.750
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.748
3lcc SAHThiocyanate methyltransferase 1 / 0.747
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.744
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.744
5je4 SAHMethyl transferase / 0.739
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.736
3ldg SAHUncharacterized protein / 0.735
1nw5 SAMModification methylase RsrI 2.1.1.72 0.731
7mht SAHModification methylase HhaI 2.1.1.37 0.730
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.726
3ou2 SAHSAM-dependent methyltransferase / 0.725
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.725
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.722
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.722
4nec SAHPutative SAM-dependent methyltransferase / 0.722
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.721
2cww SAHUncharacterized protein / 0.720
2np7 NEAModification methylase TaqI 2.1.1.72 0.720
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.720
1eg2 MTAModification methylase RsrI 2.1.1.72 0.719
3tm4 SAMUncharacterized protein / 0.718
1ori SAHProtein arginine N-methyltransferase 1 / 0.717
2f8l SAMLmo1582 protein / 0.714
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.713
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.713
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.712
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.712
2c7q SAHModification methylase HhaI 2.1.1.37 0.711
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.711
2z6u SAHModification methylase HhaI 2.1.1.37 0.708
1y9d FADPyruvate oxidase 1.2.3.3 0.707
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.706
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.705
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.705
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.705
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.705
3duw SAHO-methyltransferase, putative / 0.703
3mht SAHModification methylase HhaI 2.1.1.37 0.703
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.701
2yqz SAMUncharacterized protein / 0.701
4rtm SAMDNA adenine methylase 2.1.1.72 0.700
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.700
2np6 NEAModification methylase TaqI 2.1.1.72 0.698
5bxy SAHPutative RNA methylase family UPF0020 / 0.698
1nw6 SFGModification methylase RsrI 2.1.1.72 0.697
4lwp SAHArginine N-methyltransferase, putative / 0.697
2i9k SAHModification methylase HhaI 2.1.1.37 0.696
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.695
1uay ADNOxidoreductase / 0.694
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.694
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.694
3go4 SAHUncharacterized protein / 0.693
5epe SAHUncharacterized protein / 0.693
2h39 ADQADP-glucose phosphorylase / 0.692
2zcj SAHModification methylase HhaI 2.1.1.37 0.692
4rtq SAHDNA adenine methylase 2.1.1.72 0.692
10mh SAHModification methylase HhaI 2.1.1.37 0.691
1wy7 SAHUncharacterized protein / 0.691
2hnk SAHSAM-dependent O-methyltransferase / 0.691
4kvz SAHPtnL protein / 0.691
4yv2 S4MSpermidine synthase, putative / 0.691
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.690
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.690
4gf5 SAHCalS11 / 0.690
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.690
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.688
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.688
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.688
3fri SAH16S rRNA methylase / 0.688
4rto SFGDNA adenine methylase 2.1.1.72 0.688
4yv1 S4MSpermidine synthase, putative / 0.688
4rtr SAMDNA adenine methylase 2.1.1.72 0.687
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.687
2uyh SAHModification methylase HhaI 2.1.1.37 0.686
3cbg SAHO-methyltransferase / 0.686
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.686
1aqi SAHModification methylase TaqI 2.1.1.72 0.685
2qe6 SAMUncharacterized protein / 0.685
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.685
1g60 SAMModification methylase MboII 2.1.1.72 0.684
1skm SAHModification methylase HhaI 2.1.1.37 0.684
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.684
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.683
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.683
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.683
4rtl SFGDNA adenine methylase 2.1.1.72 0.683
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.682
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.681
4kwc SAHMethyltransferase domain family / 0.681
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.681
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.681
2yg4 FADPutrescine oxidase / 0.679
3gu3 SAHMethyltransferase / 0.678
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.678
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.677
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.677
4mb2 ATPUncharacterized protein / 0.677
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.676
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.676
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.675
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.675
1txz APRProbable ADP-ribose 1''-phosphate phosphatase YML087W 3.1.3.84 0.673
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.672
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.672
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.672
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.671
4rts SAMDNA adenine methylase 2.1.1.72 0.671
3emd SFGMethyltransferase / 0.670
4hh4 SAHCcbJ / 0.670
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.670
3s1s SAHRestriction endonuclease BpuSI / 0.669
4fn4 NADShort chain dehydrogenase / 0.668
1fjx SAHModification methylase HhaI 2.1.1.37 0.667
1g38 NEAModification methylase TaqI 2.1.1.72 0.667
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.667
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.667
2gsd NADFormate dehydrogenase / 0.666
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.665
4c03 SFGProtein arginine N-methyltransferase 6 / 0.665
1orh SAHProtein arginine N-methyltransferase 1 / 0.664
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.664
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.664
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.663
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.663
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.662
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.662
1ve3 SAMUncharacterized protein / 0.661
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.661
4ctk SAMGenome polyprotein / 0.661
4gol SA8DNA adenine methylase 2.1.1.72 0.661
8mht SAHModification methylase HhaI 2.1.1.37 0.661
3c3y SAHO-methyltransferase / 0.660
5f8f SFGPossible transcriptional regulatory protein / 0.660
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.659
4ube 2FAAdenosine kinase 2.7.1.20 0.659
2zif SAMMethyltransferase / 0.658
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.658
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.657
2xvm SAHTellurite methyltransferase 2.1.1.265 0.657
3tlj SAHUncharacterized protein / 0.657
3tos SAHCalS11 / 0.657
1m2j APRNAD-dependent protein deacylase 1 / 0.656
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.656
4mht SAHModification methylase HhaI 2.1.1.37 0.656
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.655
4uy6 SAHHistidine N-alpha-methyltransferase / 0.655
2px5 SAHGenome polyprotein 2.7.7.48 0.654
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.654
4ctj SAMGenome polyprotein / 0.654
4tlx FDAKtzI / 0.654
2x2r X2OKinesin-like protein KIF11 / 0.653
4wx1 FDAUDP-galactopyranose mutase / 0.653
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.653
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.652
2ih5 NEAModification methylase TaqI 2.1.1.72 0.652
2px2 SAHGenome polyprotein 2.7.7.48 0.652
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.652
5bp7 SAHSAM-dependent methyltransferase / 0.652
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.651
9mht SAHModification methylase HhaI 2.1.1.37 0.651
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.650
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.650
3ou6 SAMSAM-dependent methyltransferase / 0.650
4rtn SAHDNA adenine methylase 2.1.1.72 0.650