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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
5bp7 SAH SAM-dependent methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5bp7 SAHSAM-dependent methyltransferase / 1.017
5epe SAHUncharacterized protein / 0.987
2qe6 SAMUncharacterized protein / 0.755
4nec SAHPutative SAM-dependent methyltransferase / 0.751
3t7s SAMUncharacterized protein / 0.748
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.747
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.747
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.746
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.741
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.738
2yqz SAMUncharacterized protein / 0.737
3kkz SAMUncharacterized protein / 0.736
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.729
3lcc SAHThiocyanate methyltransferase 1 / 0.726
5je2 SAHMethyl transferase / 0.726
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.725
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.720
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.719
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.719
4c03 SFGProtein arginine N-methyltransferase 6 / 0.717
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.716
2p35 SAHTrans-aconitate 2-methyltransferase / 0.710
4fr0 SAMArsenic methyltransferase / 0.708
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.708
3e23 SAMUncharacterized protein / 0.707
3ou2 SAHSAM-dependent methyltransferase / 0.707
3fri SAH16S rRNA methylase / 0.706
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.705
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.705
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.703
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.702
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.702
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.702
5je4 SAHMethyl transferase / 0.701
2gs9 SAHUncharacterized protein / 0.698
5je3 SAHMethyl transferase / 0.698
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.696
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.696
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.695
4qpp SAHProtein arginine N-methyltransferase 6 / 0.694
4kwc SAHMethyltransferase domain family / 0.693
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.692
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.691
3e8s SAHUncharacterized protein / 0.689
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.689
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.688
4kvz SAHPtnL protein / 0.688
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.688
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.686
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.685
3p9k SAHCaffeic acid O-methyltransferase / 0.685
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.685
2i9k SAHModification methylase HhaI 2.1.1.37 0.681
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.678
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.678
3lst SAHCalO1 / 0.678
4hh4 SAHCcbJ / 0.678
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.678
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.676
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.676
1v5e FADPyruvate oxidase / 0.675
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.675
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.674
4e2x SAHMethyltransferase / 0.674
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.674
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.673
5bp9 SAHPutative methyltransferase protein / 0.673
4c04 SFGProtein arginine N-methyltransferase 6 / 0.672
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.672
5f8f SFGPossible transcriptional regulatory protein / 0.669
3g5q FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.668
5jdz SAHMethyl transferase / 0.668
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.666
3c3y SAHO-methyltransferase / 0.665
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.665
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.665
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.664
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.664
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.663
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.663
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.663
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.662
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.662
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.661
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.661
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.660
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.660
4lwp SAHArginine N-methyltransferase, putative / 0.660
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.660
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.659
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.659
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.659
3t0i SAHPutative methyltransferase / 0.659
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.658
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.658
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.658
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.657
2ih5 NEAModification methylase TaqI 2.1.1.72 0.657
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.657
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.655
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.655
1rsg FADPolyamine oxidase FMS1 / 0.654
2zif SAMMethyltransferase / 0.654
4dkj SAHCytosine-specific methyltransferase / 0.654
4guu FA9Lysine-specific histone demethylase 1B 1 0.654
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.654
4qnv GEKtRNA U34 carboxymethyltransferase / 0.654
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.653
5eku SAHArginine N-methyltransferase, putative / 0.653
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.652
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.651
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.651
1f3l SAHProtein arginine N-methyltransferase 3 / 0.650
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.650