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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
1nw6 SFG Modification methylase RsrI 2.1.1.72

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1nw6 SFGModification methylase RsrI 2.1.1.72 1.000
1eg2 MTAModification methylase RsrI 2.1.1.72 0.804
1nw5 SAMModification methylase RsrI 2.1.1.72 0.801
2ore SAHDNA adenine methylase 2.1.1.72 0.768
4rtq SAHDNA adenine methylase 2.1.1.72 0.752
4gol SA8DNA adenine methylase 2.1.1.72 0.741
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.741
1boo SAHModification methylase PvuII 2.1.1.113 0.738
4rts SAMDNA adenine methylase 2.1.1.72 0.738
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.730
4rtk SAHDNA adenine methylase 2.1.1.72 0.730
4gbe SAHDNA adenine methylase 2.1.1.72 0.724
2i9k SAHModification methylase HhaI 2.1.1.37 0.720
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.718
3mht SAHModification methylase HhaI 2.1.1.37 0.717
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.713
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.712
4rtj SFGDNA adenine methylase 2.1.1.72 0.711
4rto SFGDNA adenine methylase 2.1.1.72 0.709
2c7q SAHModification methylase HhaI 2.1.1.37 0.708
1yf3 SAHDNA adenine methylase / 0.707
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.706
4fr0 SAMArsenic methyltransferase / 0.706
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.705
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.704
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.703
10mh SAHModification methylase HhaI 2.1.1.37 0.701
1g1a NADdTDP-glucose 4,6-dehydratase / 0.700
2g1p SAHDNA adenine methylase 2.1.1.72 0.697
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.697
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.696
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.696
3ldg SAHUncharacterized protein / 0.696
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.695
4rtn SAHDNA adenine methylase 2.1.1.72 0.695
5bxy SAHPutative RNA methylase family UPF0020 / 0.695
4rtr SAMDNA adenine methylase 2.1.1.72 0.694
1skm SAHModification methylase HhaI 2.1.1.37 0.693
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.693
2zif SAMMethyltransferase / 0.690
4rtl SFGDNA adenine methylase 2.1.1.72 0.690
4rtm SAMDNA adenine methylase 2.1.1.72 0.689
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.688
2uyh SAHModification methylase HhaI 2.1.1.37 0.688
2z6u SAHModification methylase HhaI 2.1.1.37 0.686
4yac NAIC alpha-dehydrogenase / 0.684
1uay ADNOxidoreductase / 0.683
2hmv ADPKtr system potassium uptake protein A / 0.681
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.681
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.680
5mht SAHModification methylase HhaI 2.1.1.37 0.680
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.679
2o06 MTASpermidine synthase 2.5.1.16 0.678
2o07 MTASpermidine synthase 2.5.1.16 0.678
4yv2 S4MSpermidine synthase, putative / 0.678
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.677
3tm4 SAMUncharacterized protein / 0.677
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.676
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.674
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.673
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.672
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.671
9mht SAHModification methylase HhaI 2.1.1.37 0.671
1mht SAHModification methylase HhaI 2.1.1.37 0.670
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.670
4nzh FADL-ornithine N(5)-monooxygenase / 0.670
4yag NAIC alpha-dehydrogenase / 0.670
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.670
4rtp SAMDNA adenine methylase 2.1.1.72 0.669
4poo SAMPutative RNA methylase / 0.668
1fjx SAHModification methylase HhaI 2.1.1.37 0.667
2zcj SAHModification methylase HhaI 2.1.1.37 0.666
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.664
2hnk SAHSAM-dependent O-methyltransferase / 0.664
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.662
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.662
1g38 NEAModification methylase TaqI 2.1.1.72 0.661
2yy7 NADL-threonine dehydrogenase / 0.661
2f8l SAMLmo1582 protein / 0.660
2ih5 NEAModification methylase TaqI 2.1.1.72 0.660
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.659
2np6 NEAModification methylase TaqI 2.1.1.72 0.659
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.659
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.659
3wdm ADN4-phosphopantoate--beta-alanine ligase 6.3.2.36 0.659
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.658
2np7 NEAModification methylase TaqI 2.1.1.72 0.658
3ldf SAHUncharacterized protein / 0.658
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.657
1h81 FADPolyamine oxidase 1.5.3.14 0.656
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.656
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.656
7mht SAHModification methylase HhaI 2.1.1.37 0.656
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.655
1wy7 SAHUncharacterized protein / 0.653
3fri SAH16S rRNA methylase / 0.653
4gh5 NADShort-chain dehydrogenase/reductase SDR / 0.653
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.652
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.652
4b63 FADL-ornithine N(5)-monooxygenase / 0.652
1ori SAHProtein arginine N-methyltransferase 1 / 0.651
3rw9 DSHSpermidine synthase 2.5.1.16 0.651
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.650
3s1s SAHRestriction endonuclease BpuSI / 0.650
3wv7 ADPHmd co-occurring protein HcgE / 0.650
3wv8 ATPHmd co-occurring protein HcgE / 0.650
4qi4 FADCellobiose dehydrogenase / 0.650