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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
1nw5 SAM Modification methylase RsrI 2.1.1.72

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1nw5 SAMModification methylase RsrI 2.1.1.72 1.051
1g60 SAMModification methylase MboII 2.1.1.72 0.852
1eg2 MTAModification methylase RsrI 2.1.1.72 0.833
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.819
3ldg SAHUncharacterized protein / 0.814
3tm4 SAMUncharacterized protein / 0.810
2g1p SAHDNA adenine methylase 2.1.1.72 0.803
1nw6 SFGModification methylase RsrI 2.1.1.72 0.801
4rtk SAHDNA adenine methylase 2.1.1.72 0.795
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.780
4gbe SAHDNA adenine methylase 2.1.1.72 0.777
1boo SAHModification methylase PvuII 2.1.1.113 0.765
2ore SAHDNA adenine methylase 2.1.1.72 0.765
4rtj SFGDNA adenine methylase 2.1.1.72 0.757
3tm5 SFGUncharacterized protein / 0.752
2zif SAMMethyltransferase / 0.751
2c7q SAHModification methylase HhaI 2.1.1.37 0.750
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.745
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.744
2i9k SAHModification methylase HhaI 2.1.1.37 0.743
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.742
1yf3 SAHDNA adenine methylase / 0.738
2pxa SAHGenome polyprotein 2.7.7.48 0.738
3ldf SAHUncharacterized protein / 0.735
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.732
2zcj SAHModification methylase HhaI 2.1.1.37 0.732
3mht SAHModification methylase HhaI 2.1.1.37 0.732
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.731
2uyh SAHModification methylase HhaI 2.1.1.37 0.730
5mht SAHModification methylase HhaI 2.1.1.37 0.730
10mh SAHModification methylase HhaI 2.1.1.37 0.729
4rtl SFGDNA adenine methylase 2.1.1.72 0.724
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.723
4rtm SAMDNA adenine methylase 2.1.1.72 0.721
2z6u SAHModification methylase HhaI 2.1.1.37 0.720
3qv2 SAH5-cytosine DNA methyltransferase / 0.718
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.718
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.718
1mht SAHModification methylase HhaI 2.1.1.37 0.716
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.715
1skm SAHModification methylase HhaI 2.1.1.37 0.714
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.714
4dmg SAMUncharacterized protein / 0.714
7mht SAHModification methylase HhaI 2.1.1.37 0.714
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.712
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.711
4rtq SAHDNA adenine methylase 2.1.1.72 0.711
4dkj SAHCytosine-specific methyltransferase / 0.710
4rtp SAMDNA adenine methylase 2.1.1.72 0.710
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.705
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.705
2f8l SAMLmo1582 protein / 0.704
3eey SAMrRNA methylase / 0.704
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.704
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.703
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.703
2yxl SFG450aa long hypothetical fmu protein / 0.702
4rto SFGDNA adenine methylase 2.1.1.72 0.701
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.699
4mht SAHModification methylase HhaI 2.1.1.37 0.699
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.698
1r6a SAHGenome polyprotein 2.7.7.48 0.697
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.696
2hmv ADPKtr system potassium uptake protein A / 0.695
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.694
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.694
8mht SAHModification methylase HhaI 2.1.1.37 0.694
4gol SA8DNA adenine methylase 2.1.1.72 0.693
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.693
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.692
2pt6 S4MSpermidine synthase / 0.692
4poo SAMPutative RNA methylase / 0.692
4rtr SAMDNA adenine methylase 2.1.1.72 0.691
5jdz SAHMethyl transferase / 0.691
9mht SAHModification methylase HhaI 2.1.1.37 0.685
1fjx SAHModification methylase HhaI 2.1.1.37 0.682
4yv2 S4MSpermidine synthase, putative / 0.682
1uay ADNOxidoreductase / 0.681
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.681
4nec SAHPutative SAM-dependent methyltransferase / 0.680
4yv1 S4MSpermidine synthase, putative / 0.680
4fr0 SAMArsenic methyltransferase / 0.679
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.678
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.678
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.677
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.677
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.676
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.672
2px2 SAHGenome polyprotein 2.7.7.48 0.671
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.671
4rts SAMDNA adenine methylase 2.1.1.72 0.671
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.671
4yac NAIC alpha-dehydrogenase / 0.671
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.670
3ely SAHMethyltransferase / 0.670
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.670
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.669
4yv0 S4MSpermidine synthase, putative / 0.669
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.667
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.667
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.667
5dto SAHGenome polyprotein / 0.667
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.666
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.666
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.665
3eld SFGMethyltransferase / 0.665
3elu SAMMethyltransferase / 0.665
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.665
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.665
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.664
1l9k SAHGenome polyprotein 2.7.7.48 0.664
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.664
3rw9 DSHSpermidine synthase 2.5.1.16 0.663
3evg SAHGenome polyprotein 2.1.1.56 0.662
3lcc SAHThiocyanate methyltransferase 1 / 0.662
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.662
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.661
4c05 SAHProtein arginine N-methyltransferase 6 / 0.660
1wy7 SAHUncharacterized protein / 0.659
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.658
3lkz SFGGenome polyprotein / 0.658
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.657
3lov FADProtoporphyrinogen oxidase / 0.657
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.657
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.656
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.656
2cww SAHUncharacterized protein / 0.655
2hnk SAHSAM-dependent O-methyltransferase / 0.655
2ih2 NEAModification methylase TaqI 2.1.1.72 0.655
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.655
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.653
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.653
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.653
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.652
3evb SAHGenome polyprotein 2.1.1.56 0.652
2bm9 SAMCephalosporin hydroxylase CmcI / 0.651
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.651
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.650