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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
3aky AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3aky AP5Adenylate kinase / 1.809
2aky AP5Adenylate kinase / 1.685
4w5j AP5Adenylate kinase / 1.301
4mkg AP5Adenylate kinase / 1.294
4mkf AP5Adenylate kinase / 1.286
3dkv AP5Adenylate kinase / 1.252
4nu0 AP5Adenylate kinase / 1.234
2oo7 AP5Adenylate kinase / 1.146
3dl0 AP5Adenylate kinase / 1.113
4qbh AP5Adenylate kinase / 1.083
2osb AP5Adenylate kinase / 1.078
2eu8 AP5Adenylate kinase / 1.070
1p3j AP5Adenylate kinase / 1.065
2qaj AP5Adenylate kinase / 1.055
4tyq AP5Adenylate kinase / 1.023
4qbi AP5Adenylate kinase / 1.009
1s3g AP5Adenylate kinase / 0.995
1zio AP5Adenylate kinase / 0.980
4mkh AP5Adenylate kinase / 0.899
4x8l AP5Adenylate kinase / 0.871
1ake AP5Adenylate kinase / 0.831
4x8o AP5Adenylate kinase / 0.830
4jky ADPAdenylate kinase / 0.822
4typ AP5Adenylate kinase / 0.821
4jl8 ADPAdenylate kinase / 0.805
4jl6 ADPAdenylate kinase / 0.800
4jlo ADPAdenylate kinase / 0.799
4ike ADPAdenylate kinase / 0.798
2rgx AP5Adenylate kinase / 0.793
3hpr AP5Adenylate kinase / 0.756
4qbf AP5Adenylate kinase / 0.752
3hpq AP5Adenylate kinase / 0.751
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.731
2eck ADPAdenylate kinase / 0.728
4jlb ADPAdenylate kinase / 0.728
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.721
1dvr ATFAdenylate kinase / 0.706
4jlp ADPAdenylate kinase / 0.706
1e4v AP5Adenylate kinase / 0.704
3wyf GTPGTP-binding nuclear protein / 0.691
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.691
3tqc ADPPantothenate kinase / 0.690
4ohv ANPProtein clpf-1 / 0.685
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.680
1zm7 TTPDeoxynucleoside kinase / 0.680
1mmg AGSMyosin-2 heavy chain / 0.679
2fg5 GNPRas-related protein Rab-31 / 0.673
4dvg GSPRho family GTPase / 0.672
4jl5 ADPAdenylate kinase / 0.665
4cf7 ADPAdenylate kinase / 0.662
2y6p CTP3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 0.660
3qfs NAPNADPH--cytochrome P450 reductase / 0.660
3vth APCCarbamoyltransferase / 0.660
3rv4 ADPBiotin carboxylase 6.3.4.14 0.659
4pjj ADPUnconventional myosin-VI / 0.659
1e4y AP5Adenylate kinase / 0.658
4qbg AP5Adenylate kinase / 0.657
1a2b GSPTransforming protein RhoA / 0.656
4ffl ADPUncharacterized protein / 0.656
1fmw ATPMyosin-2 heavy chain / 0.655
3qft NAPNADPH--cytochrome P450 reductase / 0.655
3af1 GDPPantothenate kinase 2.7.1.33 0.651
4rkf GNPRas-related protein Rab-3 / 0.650