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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
3vc1 SAH Geranyl diphosphate 2-C-methyltransferase 2.1.1.255

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 1.084
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 1.026
2zfu SAHRibosomal RNA-processing protein 8 / 0.774
4pne SAHMethyltransferase-like protein / 0.772
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.749
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.738
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.727
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.724
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.721
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.717
3fri SAH16S rRNA methylase / 0.715
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.715
2yqz SAMUncharacterized protein / 0.708
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.708
3t7s SAMUncharacterized protein / 0.708
4nec SAHPutative SAM-dependent methyltransferase / 0.706
4x3q SAHSibL / 0.705
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.704
3e23 SAMUncharacterized protein / 0.703
4kvz SAHPtnL protein / 0.702
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.699
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.697
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.696
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.696
3e8s SAHUncharacterized protein / 0.695
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.694
4hh4 SAHCcbJ / 0.694
4f84 SAMGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.693
4f86 SFGGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.693
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.690
5epe SAHUncharacterized protein / 0.690
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.689
1ve3 SAMUncharacterized protein / 0.688
3t7t SAHUncharacterized protein / 0.688
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.687
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.686
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.686
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.684
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.683
4e2x SAHMethyltransferase / 0.682
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.682
3go4 SAHUncharacterized protein / 0.681
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.680
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.679
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.678
3lst SAHCalO1 / 0.677
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.676
3p9k SAHCaffeic acid O-methyltransferase / 0.675
2gs9 SAHUncharacterized protein / 0.674
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.674
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.674
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.674
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.674
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.674
5bxy SAHPutative RNA methylase family UPF0020 / 0.672
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.671
1ryd NDPGlucose--fructose oxidoreductase 1.1.99.28 0.670
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.669
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.669
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.668
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.668
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.666
3ou2 SAHSAM-dependent methyltransferase / 0.666
5bp9 SAHPutative methyltransferase protein / 0.666
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.663
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.663
5je2 SAHMethyl transferase / 0.663
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.661
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.661
2qe6 SAMUncharacterized protein / 0.661
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.661
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.660
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.660
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.659
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.659
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.655
4rvd SAMD-mycarose 3-C-methyltransferase / 0.655
1nc1 MTH5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase 3.2.2.9 0.654
5jdz SAHMethyl transferase / 0.654
5je3 SAHMethyl transferase / 0.654
2xvm SAHTellurite methyltransferase 2.1.1.265 0.653
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.653
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.652
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.652
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.650
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.650