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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
4poo SAM Putative RNA methylase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4poo SAMPutative RNA methylase / 1.105
3eey SAMrRNA methylase / 0.941
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.762
3lby SAHUncharacterized protein / 0.758
1yf3 SAHDNA adenine methylase / 0.753
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.750
4dmg SAMUncharacterized protein / 0.744
1skm SAHModification methylase HhaI 2.1.1.37 0.730
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.730
4rtj SFGDNA adenine methylase 2.1.1.72 0.727
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.726
2eg5 SAH7-methylxanthosine synthase 1 / 0.723
2i9k SAHModification methylase HhaI 2.1.1.37 0.719
2zcj SAHModification methylase HhaI 2.1.1.37 0.718
3mht SAHModification methylase HhaI 2.1.1.37 0.716
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.714
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.711
3qv2 SAH5-cytosine DNA methyltransferase / 0.709
5mht SAHModification methylase HhaI 2.1.1.37 0.709
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.708
2uyh SAHModification methylase HhaI 2.1.1.37 0.708
3ldg SAHUncharacterized protein / 0.708
1boo SAHModification methylase PvuII 2.1.1.113 0.704
4dkj SAHCytosine-specific methyltransferase / 0.704
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.702
2cww SAHUncharacterized protein / 0.698
7mht SAHModification methylase HhaI 2.1.1.37 0.697
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.694
2c7q SAHModification methylase HhaI 2.1.1.37 0.693
2z6u SAHModification methylase HhaI 2.1.1.37 0.693
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.693
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.692
1nw5 SAMModification methylase RsrI 2.1.1.72 0.692
1g60 SAMModification methylase MboII 2.1.1.72 0.691
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.691
3ldf SAHUncharacterized protein / 0.690
3vyw SAMUncharacterized protein / 0.690
2hnk SAHSAM-dependent O-methyltransferase / 0.689
2o06 MTASpermidine synthase 2.5.1.16 0.689
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.689
2f8l SAMLmo1582 protein / 0.688
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.688
1fjx SAHModification methylase HhaI 2.1.1.37 0.687
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.685
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.685
10mh SAHModification methylase HhaI 2.1.1.37 0.683
2g1p SAHDNA adenine methylase 2.1.1.72 0.683
4gbe SAHDNA adenine methylase 2.1.1.72 0.683
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.682
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.679
3rw9 DSHSpermidine synthase 2.5.1.16 0.679
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.679
8mht SAHModification methylase HhaI 2.1.1.37 0.678
4rtm SAMDNA adenine methylase 2.1.1.72 0.676
3ou6 SAMSAM-dependent methyltransferase / 0.675
4e2x SAHMethyltransferase / 0.675
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.674
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.674
1wy7 SAHUncharacterized protein / 0.673
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.672
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.672
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.671
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.670
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.670
1nw6 SFGModification methylase RsrI 2.1.1.72 0.668
2hmv ADPKtr system potassium uptake protein A / 0.667
4hh4 SAHCcbJ / 0.667
1eg2 MTAModification methylase RsrI 2.1.1.72 0.666
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.666
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.665
4gf5 SAHCalS11 / 0.665
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.664
3sx2 NADUncharacterized protein / 0.663
5bxy SAHPutative RNA methylase family UPF0020 / 0.663
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.660
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.659
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.659
4rtp SAMDNA adenine methylase 2.1.1.72 0.659
4mht SAHModification methylase HhaI 2.1.1.37 0.658
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.658
3qft NAPNADPH--cytochrome P450 reductase / 0.656
5je3 SAHMethyl transferase / 0.656
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.655
1uay ADNOxidoreductase / 0.655
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.655
3qfs NAPNADPH--cytochrome P450 reductase / 0.655
5je4 SAHMethyl transferase / 0.655
9mht SAHModification methylase HhaI 2.1.1.37 0.655
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.654
5jdz SAHMethyl transferase / 0.654
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.653
1ve3 SAMUncharacterized protein / 0.652
1y9d FADPyruvate oxidase 1.2.3.3 0.652
2yg4 FADPutrescine oxidase / 0.652
3lbf SAHProtein-L-isoaspartate O-methyltransferase 2.1.1.77 0.652
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.652
2np6 NEAModification methylase TaqI 2.1.1.72 0.651