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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
1s3g AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1s3g AP5Adenylate kinase / 1.819
2oo7 AP5Adenylate kinase / 1.139
4qbh AP5Adenylate kinase / 1.129
1p3j AP5Adenylate kinase / 1.123
2eu8 AP5Adenylate kinase / 1.115
2qaj AP5Adenylate kinase / 1.075
3dl0 AP5Adenylate kinase / 1.066
4mkg AP5Adenylate kinase / 1.063
3aky AP5Adenylate kinase / 0.995
1e4v AP5Adenylate kinase / 0.977
2osb AP5Adenylate kinase / 0.955
3dkv AP5Adenylate kinase / 0.949
4w5j AP5Adenylate kinase / 0.945
4nu0 AP5Adenylate kinase / 0.931
2aky AP5Adenylate kinase / 0.926
1zio AP5Adenylate kinase / 0.917
4mkh AP5Adenylate kinase / 0.907
4tyq AP5Adenylate kinase / 0.863
4qbf AP5Adenylate kinase / 0.858
2rgx AP5Adenylate kinase / 0.856
1ake AP5Adenylate kinase / 0.824
4cf7 ADPAdenylate kinase / 0.805
4jky ADPAdenylate kinase / 0.805
4ike ADPAdenylate kinase / 0.804
4mkf AP5Adenylate kinase / 0.796
4jld ADPAdenylate kinase / 0.787
4jl6 ADPAdenylate kinase / 0.775
4x8l AP5Adenylate kinase / 0.762
4jl5 ADPAdenylate kinase / 0.761
4jlo ADPAdenylate kinase / 0.760
4dxa GSPRas-related protein Rap-1b / 0.754
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.751
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.732
4jl8 ADPAdenylate kinase / 0.728
1e4y AP5Adenylate kinase / 0.726
5d3q GDPDynamin-1 3.6.5.5 0.721
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.718
3hpr AP5Adenylate kinase / 0.712
4jlb ADPAdenylate kinase / 0.712
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.710
3tlx ADPAdenylate kinase 2 / 0.705
2eck ADPAdenylate kinase / 0.698
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.695
4qbi AP5Adenylate kinase / 0.695
1ow3 GDPTransforming protein RhoA / 0.694
4jsy GTPMetallophosphoesterase / 0.693
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.691
4l8g GDPGTPase KRas / 0.690
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.687
4typ AP5Adenylate kinase / 0.683
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.681
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.677
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.677
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.677
3r9i ADPSeptum site-determining protein MinD / 0.676
4dzz ADPPlasmid partitioning protein ParF / 0.676
4hse ADPChaperone protein ClpB / 0.676
4xvu ATPATPase GET3 / 0.672
2uyi ADPKinesin-like protein KIF11 / 0.671
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.670
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.669
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.669
4epw GDPGTPase KRas / 0.668
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.666
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.666
4o2r GDPGTP-binding protein Rheb / 0.666
2dr3 ADPUPF0273 protein PH0284 / 0.665
4jlp ADPAdenylate kinase / 0.663
3cf0 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.662
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.658
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
2j9l ATPH(+)/Cl(-) exchange transporter 5 / 0.657
2zfi ADPKinesin-like protein KIF1A / 0.657
2iut AGSDNA translocase FtsK / 0.656
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.654
3dzd ADPTranscriptional regulator (NtrC family) / 0.654
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.654
5k5z ANPUncharacterized protein / 0.653
1oix GDPRas-related protein Rab-11A / 0.652
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.650