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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
4jl8 ADP Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4jl8 ADPAdenylate kinase / 1.284
4jlb ADPAdenylate kinase / 1.106
4x8l AP5Adenylate kinase / 0.990
4qbh AP5Adenylate kinase / 0.933
4qbg AP5Adenylate kinase / 0.922
3hpq AP5Adenylate kinase / 0.899
4jlp ADPAdenylate kinase / 0.850
2qaj AP5Adenylate kinase / 0.825
4qbi AP5Adenylate kinase / 0.825
2aky AP5Adenylate kinase / 0.822
1e4y AP5Adenylate kinase / 0.815
4mkh AP5Adenylate kinase / 0.809
3aky AP5Adenylate kinase / 0.805
4jla ADPAdenylate kinase / 0.805
4x8o AP5Adenylate kinase / 0.800
1e4v AP5Adenylate kinase / 0.797
2eu8 AP5Adenylate kinase / 0.797
1zio AP5Adenylate kinase / 0.775
4nu0 AP5Adenylate kinase / 0.764
3dkv AP5Adenylate kinase / 0.760
2oo7 AP5Adenylate kinase / 0.749
4qbf AP5Adenylate kinase / 0.743
3dl0 AP5Adenylate kinase / 0.740
1s3g AP5Adenylate kinase / 0.728
4tyq AP5Adenylate kinase / 0.719
4mkf AP5Adenylate kinase / 0.715
4mkg AP5Adenylate kinase / 0.713
3hpr AP5Adenylate kinase / 0.706
1p3j AP5Adenylate kinase / 0.697
5i4n ATPTyrosine-protein kinase JAK2 / 0.686
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.678
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.675
2zvb SAHPrecorrin-3 C17-methyltransferase / 0.669
1pk8 ATPSynapsin-1 / 0.665
3tw6 ADPPyruvate carboxylase / 0.664
2eka SAHDiphthine synthase / 0.663
4fvr ATPTyrosine-protein kinase JAK2 / 0.663
2zvc SAHPrecorrin-3 C17-methyltransferase / 0.662
2fyc GDUBeta-1,4-galactosyltransferase 1 2.4.1 0.660
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.660
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.659
2z6r SAHDiphthine synthase / 0.659
4fu0 ADPD-alanine--D-alanine ligase / 0.659
3rv4 ADPBiotin carboxylase 6.3.4.14 0.657
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.657
2dxx SAHDiphthine synthase / 0.656
2e17 SAHDiphthine synthase / 0.655
2dxw SAHDiphthine synthase / 0.654
2e4n SAHDiphthine synthase / 0.654
2en5 SAHDiphthine synthase / 0.654
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.654
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.653
2ek2 SAHDiphthine synthase / 0.653
2owk SAHDiphthine synthase / 0.653
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.653
2dxv SAHDiphthine synthase / 0.652
2ejj SAHDiphthine synthase / 0.652
4p5a FADFlavin-dependent thymidylate synthase / 0.651
4x3l MTARNA 2'-O ribose methyltransferase / 0.651
2dek SAHDiphthine synthase / 0.650
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.650
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.650