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
4gf5 SAH CalS11

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4gf5 SAHCalS11 / 1.194
3tos SAHCalS11 / 1.100
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.842
3c3y SAHO-methyltransferase / 0.830
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.817
3cbg SAHO-methyltransferase / 0.800
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.789
2hnk SAHSAM-dependent O-methyltransferase / 0.764
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.750
4ce0 SAHProbable O-methyltransferase / 0.745
2br5 SAHCephalosporin hydroxylase CmcI / 0.743
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.739
2cww SAHUncharacterized protein / 0.732
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.731
2plw SAMRibosomal RNA methyltransferase, putative / 0.729
3dh0 SAMUncharacterized protein / 0.727
3vyw SAMUncharacterized protein / 0.724
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.721
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.717
2p41 SAHGenome polyprotein / 0.713
4yuz S4MSpermidine synthase, putative / 0.712
4dmg SAMUncharacterized protein / 0.711
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.710
3duw SAHO-methyltransferase, putative / 0.710
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.709
3p8z SAHGenome polyprotein 2.1.1.56 0.708
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.705
4ctk SAMGenome polyprotein / 0.705
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.704
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.702
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.702
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.700
3emd SFGMethyltransferase / 0.698
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.696
2o07 MTASpermidine synthase 2.5.1.16 0.694
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.693
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.692
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.692
2px5 SAHGenome polyprotein 2.7.7.48 0.691
3evb SAHGenome polyprotein 2.1.1.56 0.691
3eva SAHGenome polyprotein 2.1.1.56 0.690
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.690
4oa5 SAHO-methyltransferase family protein / 0.690
2pxa SAHGenome polyprotein 2.7.7.48 0.689
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.687
3eld SFGMethyltransferase / 0.687
3ou2 SAHSAM-dependent methyltransferase / 0.687
1yf3 SAHDNA adenine methylase / 0.686
4ctj SAMGenome polyprotein / 0.686
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.685
2bm9 SAMCephalosporin hydroxylase CmcI / 0.684
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.684
5eku SAHArginine N-methyltransferase, putative / 0.684
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.683
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.683
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.682
3lcc SAHThiocyanate methyltransferase 1 / 0.682
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.682
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.682
5jjs SAHGenome polyprotein / 0.682
2hms NAIKtr system potassium uptake protein A / 0.681
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.681
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.681
3wv7 ADPHmd co-occurring protein HcgE / 0.680
4dkj SAHCytosine-specific methyltransferase / 0.680
4kvz SAHPtnL protein / 0.679
4nec SAHPutative SAM-dependent methyltransferase / 0.679
2px2 SAHGenome polyprotein 2.7.7.48 0.678
3evc SAHGenome polyprotein 2.1.1.56 0.678
3p97 SAMGenome polyprotein 2.1.1.56 0.678
4fr0 SAMArsenic methyltransferase / 0.678
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.676
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.675
4kwc SAHMethyltransferase domain family / 0.674
1e6w NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.673
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.673
2wa2 SAMGenome polyprotein / 0.673
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.673
3ea4 FABAcetolactate synthase, chloroplastic 2.2.1.6 0.673
3ely SAHMethyltransferase / 0.673
4rvd SAMD-mycarose 3-C-methyltransferase / 0.673
5f2k SAHUncharacterized protein / 0.673
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.671
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.671
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.671
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.671
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.671
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.670
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.670
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.669
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.666
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.665
4poo SAMPutative RNA methylase / 0.665
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.664
3lkz SFGGenome polyprotein / 0.664
3s55 NADPutative short-chain dehydrogenase/reductase / 0.664
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.664
4k6m SAHGenome polyprotein / 0.664
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.661
3wv8 ATPHmd co-occurring protein HcgE / 0.660
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.659
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.659
4e2x SAHMethyltransferase / 0.659
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.659
3ou6 SAMSAM-dependent methyltransferase / 0.657
2y99 NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase 1.3.1.56 0.656
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.654
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.654
3tr6 SAHO-methyltransferase / 0.654
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.654
5je2 SAHMethyl transferase / 0.654
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.653
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.653
3okx SAMS-adenosyl-L-methionine-binding protein RPA0152 / 0.653
4idg NADPutative UDP-glucose 4-epimerase / 0.653
2pt6 S4MSpermidine synthase / 0.652
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.652
4yv2 S4MSpermidine synthase, putative / 0.652
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.651
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.651
2hmv ADPKtr system potassium uptake protein A / 0.651
5jjr SAHGenome polyprotein / 0.651
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.650
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.650
2ibt NEAModification methylase TaqI 2.1.1.72 0.650
3rfx NADUronate dehydrogenase / 0.650
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.650