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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
1s4d SAH Uroporphyrinogen-III C-methyltransferase 2.1.1.107

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1s4d SAHUroporphyrinogen-III C-methyltransferase 2.1.1.107 1.071
1v9a SAHUncharacterized protein / 0.880
2npn SAMPutative cobalamin synthesis related protein / 0.844
2ybo SAHMethyltransferase / 0.822
3nd1 SAHPrecorrin-6A synthase (Deacetylating) / 0.821
3nut SAHPrecorrin-3 methylase / 0.820
3ndc SAHPrecorrin-4 C(11)-methyltransferase 2.1.1.133 0.814
1cbf SAHCobalt-precorrin-4 C(11)-methyltransferase 2.1.1.271 0.804
2qbu SAHPrecorrin-2 methyltransferase / 0.799
2zvb SAHPrecorrin-3 C17-methyltransferase / 0.786
2e0n SAHPrecorrin-2 C20-methyltransferase / 0.769
2zvc SAHPrecorrin-3 C17-methyltransferase / 0.764
1vce SAHDiphthine synthase / 0.728
2ejz SAHDiphthine synthase / 0.720
2bb3 SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE) / 0.719
2pch SAHDiphthine synthase / 0.703
2e8h SAHDiphthine synthase / 0.699
2pca SAHDiphthine synthase / 0.697
2ejk SAHDiphthine synthase / 0.695
2huq SAHDiphthine synthase / 0.695
2owv SAHDiphthine synthase / 0.689
5a7y SAHtRNA (adenine(9)-N1)-methyltransferase 2.1.1.218 0.689
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.688
2eni SAHDiphthine synthase / 0.688
2p5c SAHDiphthine synthase / 0.687
2dsh SAHDiphthine synthase / 0.685
2dsi SAHDiphthine synthase / 0.684
2el0 SAHDiphthine synthase / 0.683
2eeq SAHDiphthine synthase / 0.681
2ele SAHDiphthine synthase / 0.681
2egs SAHDiphthine synthase / 0.680
2ek7 SAHDiphthine synthase / 0.680
2pcm SAHDiphthine synthase / 0.679
2owk SAHDiphthine synthase / 0.678
2dv7 SAHDiphthine synthase / 0.677
2ejj SAHDiphthine synthase / 0.677
2hux SAHDiphthine synthase / 0.676
2egl SAHDiphthine synthase / 0.675
2e07 SAHDiphthine synthase / 0.674
1kor ANPArgininosuccinate synthase / 0.673
2ek2 SAHDiphthine synthase / 0.673
2emu SAHDiphthine synthase / 0.673
2e15 SAHDiphthine synthase / 0.672
2e8q SAHDiphthine synthase / 0.672
2ed5 SAHDiphthine synthase / 0.672
2eld SAHDiphthine synthase / 0.672
2hut SAHDiphthine synthase / 0.672
2p9d SAHDiphthine synthase / 0.672
1kh3 ANPArgininosuccinate synthase / 0.671
2dek SAHDiphthine synthase / 0.671
2emr SAHDiphthine synthase / 0.671
2pb6 SAHDiphthine synthase / 0.671
2p6i SAHDiphthine synthase / 0.670
2dv5 SAHDiphthine synthase / 0.669
2pb5 SAHDiphthine synthase / 0.669
2dv3 SAHDiphthine synthase / 0.668
2egb SAHDiphthine synthase / 0.668
2ek3 SAHDiphthine synthase / 0.668
2eka SAHDiphthine synthase / 0.668
2p2x SAHDiphthine synthase / 0.668
2e4n SAHDiphthine synthase / 0.667
2p5f SAHDiphthine synthase / 0.667
2e16 SAHDiphthine synthase / 0.666
2pcg SAHDiphthine synthase / 0.666
2en5 SAHDiphthine synthase / 0.665
2pb4 SAHDiphthine synthase / 0.665
2c2a ADPSensor histidine kinase / 0.663
2dxv SAHDiphthine synthase / 0.663
2e7r SAHDiphthine synthase / 0.663
2el3 SAHDiphthine synthase / 0.663
2e08 SAHDiphthine synthase / 0.662
2e17 SAHDiphthine synthase / 0.662
1j1z ATPArgininosuccinate synthase / 0.660
2owu SAHDiphthine synthase / 0.658
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.658
4cng SAHSpoU rRNA methylase / 0.657
2pci SAHDiphthine synthase / 0.655
2p6l SAHDiphthine synthase / 0.654
4kgn SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.654
1mjh ATPUniversal stress protein MJ0577 / 0.652
3wo1 ADPAlanine--anticapsin ligase / 0.652
2e8s SAHDiphthine synthase / 0.651
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.651
3wnz ADPAlanine--anticapsin ligase / 0.651
4prx ADPDNA gyrase subunit B / 0.651
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.650
2z6r SAHDiphthine synthase / 0.650
4r8h SP1cAMP-activated global transcriptional regulator CRP / 0.650