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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
4dmg SAM Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4dmg SAMUncharacterized protein / 1.103
2cww SAHUncharacterized protein / 0.835
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.791
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.787
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.778
2hnk SAHSAM-dependent O-methyltransferase / 0.769
1yf3 SAHDNA adenine methylase / 0.766
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.765
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.757
4rtj SFGDNA adenine methylase 2.1.1.72 0.754
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.750
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.745
3tos SAHCalS11 / 0.744
4poo SAMPutative RNA methylase / 0.744
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.740
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.735
1eg2 MTAModification methylase RsrI 2.1.1.72 0.733
3ou2 SAHSAM-dependent methyltransferase / 0.730
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.729
4gbe SAHDNA adenine methylase 2.1.1.72 0.728
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.727
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.723
2g1p SAHDNA adenine methylase 2.1.1.72 0.722
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.719
3duw SAHO-methyltransferase, putative / 0.719
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.717
5je2 SAHMethyl transferase / 0.715
1nw5 SAMModification methylase RsrI 2.1.1.72 0.714
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.713
3c3y SAHO-methyltransferase / 0.711
4gf5 SAHCalS11 / 0.711
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.709
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.709
10mh SAHModification methylase HhaI 2.1.1.37 0.707
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.707
2ore SAHDNA adenine methylase 2.1.1.72 0.706
2yqz SAMUncharacterized protein / 0.702
1y9d FADPyruvate oxidase 1.2.3.3 0.701
1mht SAHModification methylase HhaI 2.1.1.37 0.700
2yxl SFG450aa long hypothetical fmu protein / 0.700
4rtm SAMDNA adenine methylase 2.1.1.72 0.700
5je4 SAHMethyl transferase / 0.700
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.700
7mht SAHModification methylase HhaI 2.1.1.37 0.698
4nec SAHPutative SAM-dependent methyltransferase / 0.696
4oa5 SAHO-methyltransferase family protein / 0.695
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.694
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.691
3ou6 SAMSAM-dependent methyltransferase / 0.691
3tr6 SAHO-methyltransferase / 0.691
4kvz SAHPtnL protein / 0.691
4kwc SAHMethyltransferase domain family / 0.690
4ft4 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.688
3qv2 SAH5-cytosine DNA methyltransferase / 0.686
4rtk SAHDNA adenine methylase 2.1.1.72 0.686
2zif SAMMethyltransferase / 0.684
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.683
2eg5 SAH7-methylxanthosine synthase 1 / 0.683
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.682
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.681
3ldf SAHUncharacterized protein / 0.681
3ldg SAHUncharacterized protein / 0.681
3t7s SAMUncharacterized protein / 0.681
4hh4 SAHCcbJ / 0.681
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.679
2f8l SAMLmo1582 protein / 0.679
3mht SAHModification methylase HhaI 2.1.1.37 0.679
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.679
1ori SAHProtein arginine N-methyltransferase 1 / 0.678
3eey SAMrRNA methylase / 0.678
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.677
5je3 SAHMethyl transferase / 0.677
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.676
3lcc SAHThiocyanate methyltransferase 1 / 0.676
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.675
3cbg SAHO-methyltransferase / 0.674
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.674
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.672
4lwp SAHArginine N-methyltransferase, putative / 0.672
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.672
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.672
3go4 SAHUncharacterized protein / 0.670
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.669
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.668
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.668
3lkz SFGGenome polyprotein / 0.668
5jdz SAHMethyl transferase / 0.668
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.667
5f8f SFGPossible transcriptional regulatory protein / 0.667
5mht SAHModification methylase HhaI 2.1.1.37 0.667
2bm9 SAMCephalosporin hydroxylase CmcI / 0.666
3t0i SAHPutative methyltransferase / 0.666
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.665
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.665
5epe SAHUncharacterized protein / 0.665
1f3l SAHProtein arginine N-methyltransferase 3 / 0.664
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.662
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.662
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.662
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.661
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.661
4h0n SAHDnmt2 / 0.661
4rtq SAHDNA adenine methylase 2.1.1.72 0.661
3fpf MTAUncharacterized protein / 0.660
2hmv ADPKtr system potassium uptake protein A / 0.659
2o06 MTASpermidine synthase 2.5.1.16 0.659
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.658
2px5 SAHGenome polyprotein 2.7.7.48 0.657
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.657
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.657
4ctk SAMGenome polyprotein / 0.657
4uy6 SAHHistidine N-alpha-methyltransferase / 0.657
5dto SAHGenome polyprotein / 0.657
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.656
3fri SAH16S rRNA methylase / 0.656
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.654
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.654
4x3q SAHSibL / 0.654
4yv0 S4MSpermidine synthase, putative / 0.653
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.652
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.652
5jjr SAHGenome polyprotein / 0.652
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.651
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.651
4ctj SAMGenome polyprotein / 0.651
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.650
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.650
4c05 SAHProtein arginine N-methyltransferase 6 / 0.650