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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
1kph SAH Cyclopropane mycolic acid synthase 1 2.1.1.79

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 1.093
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.861
4pne SAHMethyltransferase-like protein / 0.825
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.805
3ha3 SAHHydroxymycolate synthase MmaA4 2.1.1 0.805
3ha5 SFGHydroxymycolate synthase MmaA4 2.1.1 0.799
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.798
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.786
3fri SAH16S rRNA methylase / 0.784
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.780
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.780
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.776
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.772
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.769
4c03 SFGProtein arginine N-methyltransferase 6 / 0.753
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.749
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.742
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.738
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.736
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.735
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.730
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.729
3e8s SAHUncharacterized protein / 0.727
3lcc SAHThiocyanate methyltransferase 1 / 0.727
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.727
1f3l SAHProtein arginine N-methyltransferase 3 / 0.725
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.721
5je3 SAHMethyl transferase / 0.721
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.715
4hh4 SAHCcbJ / 0.715
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.714
5epe SAHUncharacterized protein / 0.712
4qpp SAHProtein arginine N-methyltransferase 6 / 0.711
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.708
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.707
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.705
2yqz SAMUncharacterized protein / 0.703
3e23 SAMUncharacterized protein / 0.703
3ou2 SAHSAM-dependent methyltransferase / 0.703
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.703
5jdz SAHMethyl transferase / 0.702
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.698
5bp7 SAHSAM-dependent methyltransferase / 0.696
3lst SAHCalO1 / 0.695
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.695
4nec SAHPutative SAM-dependent methyltransferase / 0.695
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.695
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.694
3kh5 ADPUncharacterized protein MJ1225 / 0.694
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.694
5je2 SAHMethyl transferase / 0.694
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.692
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.690
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.688
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.686
5bp9 SAHPutative methyltransferase protein / 0.686
1nc1 MTH5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase 3.2.2.9 0.681
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.681
3go4 SAHUncharacterized protein / 0.681
3t0i SAHPutative methyltransferase / 0.681
3t7s SAMUncharacterized protein / 0.679
5f2k SAHUncharacterized protein / 0.678
2xvm SAHTellurite methyltransferase 2.1.1.265 0.677
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.675
2qe6 SAMUncharacterized protein / 0.675
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.671
4e2x SAHMethyltransferase / 0.670
1yf3 SAHDNA adenine methylase / 0.669
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.668
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.668
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.667
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.666
4rvd SAMD-mycarose 3-C-methyltransferase / 0.665
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.664
3kpb SAMUncharacterized protein MJ0100 / 0.664
3rw9 DSHSpermidine synthase 2.5.1.16 0.664
3sxj SAMPutative methyltransferase / 0.664
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.660
5je4 SAHMethyl transferase / 0.660
1c0k FADD-amino-acid oxidase 1.4.3.3 0.659
4ube 2FAAdenosine kinase 2.7.1.20 0.659
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.658
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.658
4f86 SFGGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.658
3iv6 SAMUncharacterized protein / 0.657
3ldg SAHUncharacterized protein / 0.657
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.657
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.656
2wzb ADPPhosphoglycerate kinase 1 2.7.2.3 0.654
2zfu SAHRibosomal RNA-processing protein 8 / 0.653
1yon A2R2-dehydropantoate 2-reductase 1.1.1.169 0.652
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.651
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.651
2d1c NAPIsocitrate dehydrogenase [NADP] 1.1.1.42 0.650
3kkz SAMUncharacterized protein / 0.650
3o9z NADLipopolysaccaride biosynthesis protein wbpB / 0.650