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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
2egv SAM Ribosomal RNA small subunit methyltransferase E 2.1.1.193

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 1.004
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.882
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.791
2ha8 SAHProbable methyltransferase TARBP1 / 0.789
4kgn SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.784
4x3l MTARNA 2'-O ribose methyltransferase / 0.766
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.758
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.746
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.743
3gyq SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase / 0.736
5a7y SAHtRNA (adenine(9)-N1)-methyltransferase 2.1.1.218 0.731
4cnf MTASpoU rRNA methylase / 0.728
4cng SAHSpoU rRNA methylase / 0.728
2hut SAHDiphthine synthase / 0.721
2eka SAHDiphthine synthase / 0.720
2owu SAHDiphthine synthase / 0.720
2ek7 SAHDiphthine synthase / 0.719
2pcg SAHDiphthine synthase / 0.719
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.718
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.718
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.717
2ed5 SAHDiphthine synthase / 0.716
2owv SAHDiphthine synthase / 0.713
2dsi SAHDiphthine synthase / 0.711
2pb6 SAHDiphthine synthase / 0.711
2dxx SAHDiphthine synthase / 0.708
2dxv SAHDiphthine synthase / 0.705
2e07 SAHDiphthine synthase / 0.705
2e7r SAHDiphthine synthase / 0.705
2egb SAHDiphthine synthase / 0.705
2dek SAHDiphthine synthase / 0.704
2dsg SAHDiphthine synthase / 0.704
2dxw SAHDiphthine synthase / 0.704
2ehl SAHDiphthine synthase / 0.704
3oij SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.704
2dsh SAHDiphthine synthase / 0.703
2e08 SAHDiphthine synthase / 0.703
2e15 SAHDiphthine synthase / 0.703
2e17 SAHDiphthine synthase / 0.703
2owk SAHDiphthine synthase / 0.703
2p6i SAHDiphthine synthase / 0.702
2egl SAHDiphthine synthase / 0.698
2ejk SAHDiphthine synthase / 0.698
3n4k SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.698
2e16 SAHDiphthine synthase / 0.696
2eeq SAHDiphthine synthase / 0.696
4jlp ADPAdenylate kinase / 0.696
4jal SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.693
2e8s SAHDiphthine synthase / 0.691
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.691
2zvc SAHPrecorrin-3 C17-methyltransferase / 0.690
2dv5 SAHDiphthine synthase / 0.689
1j1z ATPArgininosuccinate synthase / 0.685
2yy8 SAMtRNA (cytidine(56)-2'-O)-methyltransferase / 0.685
2yy8 MTAtRNA (cytidine(56)-2'-O)-methyltransferase / 0.683
2zvb SAHPrecorrin-3 C17-methyltransferase / 0.683
2xul ATPNitrogen regulatory protein P-II / 0.681
2pci SAHDiphthine synthase / 0.678
1kh2 ATPArgininosuccinate synthase / 0.677
3nut SAHPrecorrin-3 methylase / 0.675
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.668
5hq8 SAHHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.668
4x3m ADNRNA 2'-O ribose methyltransferase / 0.667
4ynp SAMHistone-lysine N-methyltransferase ASH1L 2.1.1.43 0.667
4x8l AP5Adenylate kinase / 0.666
5ahw CMPUniversal stress protein family protein, putative / 0.664
5c77 SAHProtein arginine N-methyltransferase SFM1 / 0.664
4fu0 ADPD-alanine--D-alanine ligase / 0.663
3hgm ATPTRAP-T-associated universal stress protein TeaD / 0.661
2p5c SAHDiphthine synthase / 0.660
1rfu ADPPyridoxal kinase 2.7.1.35 0.659
1s16 ANPDNA topoisomerase 4 subunit B / 0.659
2z0y SAMRibosomal RNA small subunit methyltransferase E / 0.659
1v9o ADPSignaling protein / 0.658
3ab8 ATPUncharacterized protein / 0.658
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.657
3pdn SFGHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.657
1cbf SAHCobalt-precorrin-4 C(11)-methyltransferase 2.1.1.271 0.656
2dv3 SAHDiphthine synthase / 0.656
3bbh SFGRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.656
3qwp SAMHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.656
4jlb ADPAdenylate kinase / 0.656
4nu0 AP5Adenylate kinase / 0.656
2rgx AP5Adenylate kinase / 0.655
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.655
2ek3 SAHDiphthine synthase / 0.654
4h3z SAHtRNA (guanine-N(1)-)-methyltransferase / 0.654
5ce3 ADPProtein kinase YopO / 0.654
1ruo CMPcAMP-activated global transcriptional regulator CRP / 0.653
2aj4 ANPGalactokinase 2.7.1.6 0.653
3nie ANPMitogen-activated protein kinase / 0.653
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.653
4jl8 ADPAdenylate kinase / 0.653
2e8q SAHDiphthine synthase / 0.652
2eld SAHDiphthine synthase / 0.652
2pca SAHDiphthine synthase / 0.652
4co4 ATPNitrogen regulatory protein P-II 1 / 0.652
4ozn ATPAmmonium transporter / 0.652
4ypa SAMHistone-lysine N-methyltransferase ASH1L 2.1.1.43 0.652
2pcm SAHDiphthine synthase / 0.651
3mhy ATPNitrogen regulatory protein P-II 1 / 0.651
4jwh SAHtRNA (guanine(9)-N1)-methyltransferase / 0.651
2dv7 SAHDiphthine synthase / 0.650
2emr SAHDiphthine synthase / 0.650
3rv4 ADPBiotin carboxylase 6.3.4.14 0.650
3wo1 ADPAlanine--anticapsin ligase / 0.650
4l2i FADElectron transfer flavoprotein alpha/beta-subunit / 0.650