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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
3vc2 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
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 1.048
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 1.026
2zfu SAHRibosomal RNA-processing protein 8 / 0.817
4pne SAHMethyltransferase-like protein / 0.752
2qe6 SAMUncharacterized protein / 0.748
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.745
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.738
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.736
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.730
3fri SAH16S rRNA methylase / 0.728
3e23 SAMUncharacterized protein / 0.721
5f2k SAHUncharacterized protein / 0.719
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.717
2yqz SAMUncharacterized protein / 0.715
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.713
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.712
3e8s SAHUncharacterized protein / 0.712
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.712
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.707
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.706
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.706
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.703
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.701
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.697
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.696
4f84 SAMGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.695
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.695
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.694
4f86 SFGGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.692
4x3q SAHSibL / 0.692
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.691
2gs9 SAHUncharacterized protein / 0.691
3t7t SAHUncharacterized protein / 0.691
4nec SAHPutative SAM-dependent methyltransferase / 0.691
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.691
5jdz SAHMethyl transferase / 0.690
3t7s SAMUncharacterized protein / 0.689
5je3 SAHMethyl transferase / 0.689
5bxy SAHPutative RNA methylase family UPF0020 / 0.688
3kkz SAMUncharacterized protein / 0.687
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.687
4kvz SAHPtnL protein / 0.686
2xvm SAHTellurite methyltransferase 2.1.1.265 0.685
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.684
4rvd SAMD-mycarose 3-C-methyltransferase / 0.684
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.684
5je2 SAHMethyl transferase / 0.684
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.683
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.682
3t0i SAHPutative methyltransferase / 0.682
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.681
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.681
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.681
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.680
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.679
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.678
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.675
3lcc SAHThiocyanate methyltransferase 1 / 0.672
1ve3 SAMUncharacterized protein / 0.671
5bp9 SAHPutative methyltransferase protein / 0.671
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.670
5epe SAHUncharacterized protein / 0.670
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.669
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.666
3p9k SAHCaffeic acid O-methyltransferase / 0.665
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.663
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.663
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.662
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.662
5je4 SAHMethyl transferase / 0.662
3go4 SAHUncharacterized protein / 0.661
4hh4 SAHCcbJ / 0.660
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.659
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.659
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.658
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.657
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.656
4kwc SAHMethyltransferase domain family / 0.656
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.656
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.654
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.654
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.653
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.653
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.652
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.651
4e2x SAHMethyltransferase / 0.650