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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
3axs SFG tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 1.138
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.994
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.791
2cww SAHUncharacterized protein / 0.785
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.781
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.781
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.778
3duw SAHO-methyltransferase, putative / 0.777
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.771
2yxl SFG450aa long hypothetical fmu protein / 0.768
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.764
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.755
2g1p SAHDNA adenine methylase 2.1.1.72 0.751
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.750
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.750
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.748
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.743
3tos SAHCalS11 / 0.741
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.740
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.734
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.733
4oa5 SAHO-methyltransferase family protein / 0.732
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.731
4poo SAMPutative RNA methylase / 0.730
4rtj SFGDNA adenine methylase 2.1.1.72 0.730
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.721
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.721
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.720
2zcj SAHModification methylase HhaI 2.1.1.37 0.719
1nw6 SFGModification methylase RsrI 2.1.1.72 0.712
1yf3 SAHDNA adenine methylase / 0.712
2hnk SAHSAM-dependent O-methyltransferase / 0.710
1nw5 SAMModification methylase RsrI 2.1.1.72 0.705
4gbe SAHDNA adenine methylase 2.1.1.72 0.705
2i9k SAHModification methylase HhaI 2.1.1.37 0.703
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.703
4rto SFGDNA adenine methylase 2.1.1.72 0.702
1g60 SAMModification methylase MboII 2.1.1.72 0.701
1boo SAHModification methylase PvuII 2.1.1.113 0.700
3eey SAMrRNA methylase / 0.700
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.696
1skm SAHModification methylase HhaI 2.1.1.37 0.693
2ore SAHDNA adenine methylase 2.1.1.72 0.693
4rtk SAHDNA adenine methylase 2.1.1.72 0.693
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.693
3mht SAHModification methylase HhaI 2.1.1.37 0.689
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.688
4rtm SAMDNA adenine methylase 2.1.1.72 0.686
3cbg SAHO-methyltransferase / 0.685
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.685
1g1a NADdTDP-glucose 4,6-dehydratase / 0.684
4gf5 SAHCalS11 / 0.684
2z6u SAHModification methylase HhaI 2.1.1.37 0.683
3ldg SAHUncharacterized protein / 0.683
4rts SAMDNA adenine methylase 2.1.1.72 0.683
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.682
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.682
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.682
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.681
1eg2 MTAModification methylase RsrI 2.1.1.72 0.680
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.680
5f8f SFGPossible transcriptional regulatory protein / 0.680
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.679
1y9d FADPyruvate oxidase 1.2.3.3 0.678
4c03 SFGProtein arginine N-methyltransferase 6 / 0.678
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.678
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.676
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.675
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.675
3vyw SAMUncharacterized protein / 0.674
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.673
3c3y SAHO-methyltransferase / 0.673
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.673
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.672
2f8l SAMLmo1582 protein / 0.671
4c04 SFGProtein arginine N-methyltransferase 6 / 0.671
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.670
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.670
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.670
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.669
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.667
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.665
3tr6 SAHO-methyltransferase / 0.664
4hh4 SAHCcbJ / 0.664
3ldf SAHUncharacterized protein / 0.663
5d4u SAMUncharacterized protein MJ0489 / 0.663
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.663
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.663
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.662
4rtr SAMDNA adenine methylase 2.1.1.72 0.662
2c7q SAHModification methylase HhaI 2.1.1.37 0.660
4yac NAIC alpha-dehydrogenase / 0.660
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.658
4rtq SAHDNA adenine methylase 2.1.1.72 0.658
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.656
4rtp SAMDNA adenine methylase 2.1.1.72 0.656
1fjx SAHModification methylase HhaI 2.1.1.37 0.655
4dkj SAHCytosine-specific methyltransferase / 0.655
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.654
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.654
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.654
2eg5 SAH7-methylxanthosine synthase 1 / 0.653
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.653
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.650
4mb2 ATPUncharacterized protein / 0.650
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.650