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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
1dvr ATF Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1dvr ATFAdenylate kinase / 1.190
4jl5 ADPAdenylate kinase / 0.777
4jlo ADPAdenylate kinase / 0.740
1e4v AP5Adenylate kinase / 0.733
4mkf AP5Adenylate kinase / 0.731
4ike ADPAdenylate kinase / 0.730
4mkh AP5Adenylate kinase / 0.715
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.711
3m0e ATPTranscriptional regulator (NtrC family) / 0.710
3aky AP5Adenylate kinase / 0.706
2rgx AP5Adenylate kinase / 0.697
3oee ANPATP synthase subunit alpha, mitochondrial / 0.691
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.691
2aky AP5Adenylate kinase / 0.690
4mkg AP5Adenylate kinase / 0.690
4js0 GNPCell division control protein 42 homolog / 0.689
4nyj GNPGTPase HRas / 0.689
4mit GTPRho-related protein racC / 0.688
3dkv AP5Adenylate kinase / 0.687
3tqc ADPPantothenate kinase / 0.686
1g17 GNPRas-related protein SEC4 / 0.685
3x1z GNPRas-related protein Rap-1b / 0.683
4db1 ANPMyosin-7 / 0.683
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.680
3w3z GTPGTP-binding nuclear protein Ran / 0.680
2fna ADPUncharacterized protein / 0.678
3zfd ANPChromosome-associated kinesin KIF4 / 0.677
1v8k ANPKinesin-like protein KIF2C / 0.676
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.675
3pit GNPRas-related protein M-Ras / 0.673
2rgb GNPGTPase HRas / 0.669
2rge GNPGTPase HRas / 0.669
3i3s GNPGTPase HRas / 0.669
4l9w GNPGTPase HRas / 0.668
1ank ANPAdenylate kinase / 0.667
3k8y GNPGTPase HRas / 0.666
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.665
2osb AP5Adenylate kinase / 0.665
3rsl GNPGTPase HRas / 0.664
4c2u ANPDNA helicase / 0.664
3lbi GNPGTPase HRas / 0.660
4dlw GNPGTPase HRas / 0.659
1ake AP5Adenylate kinase / 0.657
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.656
3l8y GNPGTPase HRas / 0.656
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.656
4lhw GNPRas-related protein Rab-8A / 0.656
2bme GNPRas-related protein Rab-4A / 0.654
4ohv ANPProtein clpf-1 / 0.653
3rs7 GNPGTPase HRas / 0.652
1fmw ATPMyosin-2 heavy chain / 0.651
3ddc GNPGTPase HRas / 0.651
3oiw GNPGTPase HRas / 0.651
3r9x GNPGTPase Era / 0.651
4k81 GTPGTPase HRas / 0.651
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.650
2dft ADPShikimate kinase 2.7.1.71 0.650