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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
3dkv AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3dkv AP5Adenylate kinase / 1.791
4mkg AP5Adenylate kinase / 1.737
2qaj AP5Adenylate kinase / 1.589
2eu8 AP5Adenylate kinase / 1.553
2oo7 AP5Adenylate kinase / 1.529
4nu0 AP5Adenylate kinase / 1.443
4w5j AP5Adenylate kinase / 1.409
2osb AP5Adenylate kinase / 1.397
3dl0 AP5Adenylate kinase / 1.386
2aky AP5Adenylate kinase / 1.328
4mkf AP5Adenylate kinase / 1.295
3aky AP5Adenylate kinase / 1.252
1p3j AP5Adenylate kinase / 1.123
4mkh AP5Adenylate kinase / 1.027
4qbf AP5Adenylate kinase / 1.024
4qbg AP5Adenylate kinase / 1.017
4typ AP5Adenylate kinase / 0.983
1zio AP5Adenylate kinase / 0.976
1s3g AP5Adenylate kinase / 0.949
2rgx AP5Adenylate kinase / 0.925
4tyq AP5Adenylate kinase / 0.891
4qbi AP5Adenylate kinase / 0.844
4jlo ADPAdenylate kinase / 0.830
4jl6 ADPAdenylate kinase / 0.828
4qbh AP5Adenylate kinase / 0.828
4jky ADPAdenylate kinase / 0.801
4jl5 ADPAdenylate kinase / 0.782
4jld ADPAdenylate kinase / 0.780
1e4v AP5Adenylate kinase / 0.776
4x8l AP5Adenylate kinase / 0.776
4jl8 ADPAdenylate kinase / 0.760
1svm ATPLarge T antigen 3.6.4 0.758
3hpq AP5Adenylate kinase / 0.758
4jla ADPAdenylate kinase / 0.745
1a2b GSPTransforming protein RhoA / 0.737
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.728
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.724
4jsy GTPMetallophosphoesterase / 0.715
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.712
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.712
3hpr AP5Adenylate kinase / 0.711
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.709
4xsg GSPTransforming protein RhoA / 0.708
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.707
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.706
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.705
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.701
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.701
1svw GTPProbable GTP-binding protein EngB / 0.697
4nyi GNPGTPase HRas / 0.696
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.694
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.693
3tlx ADPAdenylate kinase 2 / 0.692
4dvg GSPRho family GTPase / 0.692
1wdt GTPElongation factor G (EF-G-2) / 0.691
3zfd ANPChromosome-associated kinesin KIF4 / 0.690
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.690
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.690
4ol0 GTPGTP-binding nuclear protein Ran / 0.688
1dvr ATFAdenylate kinase / 0.687
2vp2 DGTDeoxynucleoside kinase / 0.687
4mit GTPRho-related protein racC / 0.687
4x8o AP5Adenylate kinase / 0.686
3tjz GNPADP-ribosylation factor 1 / 0.684
4xvu ATPATPase GET3 / 0.684
1fmw ATPMyosin-2 heavy chain / 0.682
2hld ANPATP synthase subunit alpha, mitochondrial / 0.682
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.680
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.679
1sxj AGSReplication factor C subunit 1 / 0.678
3orl AGSSerine/threonine protein kinase / 0.678
4wbn GTPTubulin alpha-1B chain / 0.676
5la6 GTPTubulin alpha-1B chain / 0.676
4fvr ATPTyrosine-protein kinase JAK2 / 0.675
5itz GTPTubulin alpha-1B chain / 0.675
4jlb ADPAdenylate kinase / 0.674
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.674
4zol GTPTubulin alpha-1B chain / 0.674
5c46 GSPRas-related protein Rab-11A / 0.674
3wyf GTPGTP-binding nuclear protein / 0.672
4qm6 GTPMetallophosphoesterase / 0.671
3eg5 GNPCell division control protein 42 homolog / 0.669
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.668
2xtn GTPGTPase IMAP family member 2 / 0.668
2y6p CTP3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 0.668
2gcp GSPRho-related GTP-binding protein RhoC / 0.667
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.666
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.666
4kvg GTPRas-related protein Rap-1A / 0.666
4ihj GTPTubulin alpha-1B chain / 0.664
4tuy GTPTubulin alpha-1B chain / 0.664
4tv9 GTPTubulin alpha-1B chain / 0.664
4qnr ATPPsp operon transcriptional activator / 0.663
3vth APCCarbamoyltransferase / 0.662
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.662
4iij GTPTubulin alpha-1B chain / 0.661
1ank ANPAdenylate kinase / 0.660
1oix GDPRas-related protein Rab-11A / 0.660
2x0q ATPAlcaligin biosynthesis protein / 0.660
3bc1 GNPRas-related protein Rab-27A / 0.660
2cl6 CAGGTPase HRas / 0.659
3law GNPRas-related protein Rab-7a / 0.659
5jqg GTPTubulin alpha-1B chain / 0.659
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.658
1ixe COACitrate synthase / 0.657
1zbd GTPRas-related protein Rab-3A / 0.656
4ozn ATPAmmonium transporter / 0.656
1wa5 GTPGTP-binding nuclear protein Ran / 0.655
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.655
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.655
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.655
1kmq GNPTransforming protein RhoA / 0.654
1xjj DGTVitamin B12-dependent ribonucleotide reductase / 0.654
3kz1 GSPTransforming protein RhoA / 0.654
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.653
2vp0 TTPDeoxynucleoside kinase / 0.653
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.652
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
1b7t ADPMyosin heavy chain, striated muscle / 0.651
2eck ADPAdenylate kinase / 0.651
3dyh 721Farnesyl pyrophosphate synthase / 0.651
4xoi GTPTransforming protein RhoA / 0.651
4eht ADP2-hydroxyisocaproyl-CoA dehydratase activator / 0.650