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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
2eka SAH Diphthine synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2eka SAHDiphthine synthase / 1.151
2eh4 SAHDiphthine synthase / 1.114
2emr SAHDiphthine synthase / 1.113
2pb5 SAHDiphthine synthase / 1.113
2pcg SAHDiphthine synthase / 1.113
2ek4 SAHDiphthine synthase / 1.112
2el3 SAHDiphthine synthase / 1.112
2en5 SAHDiphthine synthase / 1.112
2e8r SAHDiphthine synthase / 1.111
2e8s SAHDiphthine synthase / 1.111
2eh5 SAHDiphthine synthase / 1.111
2pb6 SAHDiphthine synthase / 1.108
2ele SAHDiphthine synthase / 1.095
2pca SAHDiphthine synthase / 1.095
2e4n SAHDiphthine synthase / 1.094
2ed5 SAHDiphthine synthase / 1.094
2ek7 SAHDiphthine synthase / 1.094
2eld SAHDiphthine synthase / 1.094
2p9d SAHDiphthine synthase / 1.094
2dv3 SAHDiphthine synthase / 1.093
2dxx SAHDiphthine synthase / 1.093
2p5f SAHDiphthine synthase / 1.093
2eni SAHDiphthine synthase / 1.092
2p6l SAHDiphthine synthase / 1.092
2pcm SAHDiphthine synthase / 1.092
2p6k SAHDiphthine synthase / 1.091
2pck SAHDiphthine synthase / 1.090
2ek3 SAHDiphthine synthase / 1.089
2owg SAHDiphthine synthase / 1.087
2p6d SAHDiphthine synthase / 1.086
2ek2 SAHDiphthine synthase / 1.077
2egs SAHDiphthine synthase / 1.075
2eh2 SAHDiphthine synthase / 1.075
2pch SAHDiphthine synthase / 1.075
2dv5 SAHDiphthine synthase / 1.074
2dxw SAHDiphthine synthase / 1.074
2e8h SAHDiphthine synthase / 1.074
2el0 SAHDiphthine synthase / 1.074
2owk SAHDiphthine synthase / 1.074
2e08 SAHDiphthine synthase / 1.073
2p6i SAHDiphthine synthase / 1.073
1wng SAHDiphthine synthase / 1.072
2e17 SAHDiphthine synthase / 1.072
2huq SAHDiphthine synthase / 1.072
2huv SAHDiphthine synthase / 1.072
2pb4 SAHDiphthine synthase / 1.072
2eeq SAHDiphthine synthase / 1.071
2z6r SAHDiphthine synthase / 1.057
2dxv SAHDiphthine synthase / 1.056
2e07 SAHDiphthine synthase / 1.056
2e7r SAHDiphthine synthase / 1.056
2egb SAHDiphthine synthase / 1.056
2ehl SAHDiphthine synthase / 1.056
2ejj SAHDiphthine synthase / 1.056
2ejk SAHDiphthine synthase / 1.056
2dv7 SAHDiphthine synthase / 1.055
2egl SAHDiphthine synthase / 1.055
2dek SAHDiphthine synthase / 1.054
2dsg SAHDiphthine synthase / 1.054
2dsh SAHDiphthine synthase / 1.054
2e15 SAHDiphthine synthase / 1.054
2e16 SAHDiphthine synthase / 1.052
2hut SAHDiphthine synthase / 1.050
2owv SAHDiphthine synthase / 1.049
2owu SAHDiphthine synthase / 1.047
2p2x SAHDiphthine synthase / 1.045
2e8q SAHDiphthine synthase / 1.043
2dsi SAHDiphthine synthase / 1.039
2emu SAHDiphthine synthase / 1.039
2p5c SAHDiphthine synthase / 1.038
2dv4 SAHDiphthine synthase / 1.036
2pci SAHDiphthine synthase / 1.024
1vce SAHDiphthine synthase / 1.021
2hux SAHDiphthine synthase / 0.960
2hr8 SAHDiphthine synthase / 0.911
2ejz SAHDiphthine synthase / 0.832
2owf SAHDiphthine synthase / 0.740
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.720
2ed3 SAHDiphthine synthase / 0.705
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.702
1cbf SAHCobalt-precorrin-4 C(11)-methyltransferase 2.1.1.271 0.691
1jgt APCCarboxyethyl-arginine beta-lactam-synthase 6.3.3.4 0.680
2qbu SAHPrecorrin-2 methyltransferase / 0.680
3s3t ATPUniversal stress protein / 0.678
3ndc SAHPrecorrin-4 C(11)-methyltransferase 2.1.1.133 0.675
3hpq AP5Adenylate kinase / 0.672
1s16 ANPDNA topoisomerase 4 subunit B / 0.669
4rr8 A3SProbable threonine--tRNA ligase 2 6.1.1.3 0.669
1s4d SAHUroporphyrinogen-III C-methyltransferase 2.1.1.107 0.668
2ha8 SAHProbable methyltransferase TARBP1 / 0.667
4jl8 ADPAdenylate kinase / 0.663
5a7y SAHtRNA (adenine(9)-N1)-methyltransferase 2.1.1.218 0.663
3nut SAHPrecorrin-3 methylase / 0.662
2ex1 C5PAlpha-2,3/2,6-sialyltransferase/sialidase / 0.660
2e0n SAHPrecorrin-2 C20-methyltransferase / 0.659
4i0b CMPcAMP-activated global transcriptional regulator CRP / 0.659
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.659
3zu0 A12NAD 5'-nucleotidase 3.1.3.5 0.658
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.656
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.656
1v9a SAHUncharacterized protein / 0.655
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.654
5jhn SAMHistone-lysine N-methyltransferase EHMT2 / 0.654
4g36 SLULuciferin 4-monooxygenase 1.13.12.7 0.653
4rr6 A3SProbable threonine--tRNA ligase 2 6.1.1.3 0.653
4rrb A3TProbable threonine--tRNA ligase 2 6.1.1.3 0.653
4rrl A3SProbable threonine--tRNA ligase 2 6.1.1.3 0.653
1mxi SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.651
4o30 SAHProbable Histone-lysine N-methyltransferase ATXR5 2.1.1.43 0.650
4rrh A3SProbable threonine--tRNA ligase 2 6.1.1.3 0.650