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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
2osb AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2osb AP5Adenylate kinase / 1.679
2qaj AP5Adenylate kinase / 1.583
2eu8 AP5Adenylate kinase / 1.575
4mkg AP5Adenylate kinase / 1.508
2oo7 AP5Adenylate kinase / 1.486
3dkv AP5Adenylate kinase / 1.397
4mkf AP5Adenylate kinase / 1.372
3dl0 AP5Adenylate kinase / 1.344
4nu0 AP5Adenylate kinase / 1.221
4w5j AP5Adenylate kinase / 1.207
2aky AP5Adenylate kinase / 1.169
3aky AP5Adenylate kinase / 1.078
4tyq AP5Adenylate kinase / 1.015
2rgx AP5Adenylate kinase / 0.976
4qbh AP5Adenylate kinase / 0.975
1p3j AP5Adenylate kinase / 0.962
1zio AP5Adenylate kinase / 0.961
1s3g AP5Adenylate kinase / 0.955
4x8l AP5Adenylate kinase / 0.912
4qbf AP5Adenylate kinase / 0.909
4typ AP5Adenylate kinase / 0.874
4qm6 GTPMetallophosphoesterase / 0.861
4mkh AP5Adenylate kinase / 0.844
4qbi AP5Adenylate kinase / 0.836
4x8o AP5Adenylate kinase / 0.836
4jld ADPAdenylate kinase / 0.801
4jky ADPAdenylate kinase / 0.800
1ake AP5Adenylate kinase / 0.790
2eck ADPAdenylate kinase / 0.787
4qbg AP5Adenylate kinase / 0.781
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.757
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.754
4c2u ANPDNA helicase / 0.752
2ffq GSPRas-related protein Rab-6B / 0.751
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.751
4qnr ATPPsp operon transcriptional activator / 0.748
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.747
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.745
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.743
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.739
1svm ATPLarge T antigen 3.6.4 0.732
4ohx ADPProtein clpf-1 / 0.731
1a2b GSPTransforming protein RhoA / 0.726
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.724
4dso GSPGTPase KRas / 0.723
4idp GNPAtlastin-1 3.6.5 0.722
4dxa GSPRas-related protein Rap-1b / 0.721
4qxa GTPRas-related protein Rab-9A / 0.721
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.721
4v02 ATPSite-determining protein / 0.720
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.717
1z0a GDPRas-related protein Rab-2A / 0.716
4dvg GSPRho family GTPase / 0.716
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.715
3law GNPRas-related protein Rab-7a / 0.715
4y0v GDPADP-ribosylation factor 1, putative / 0.715
4ylg GDPADP-ribosylation factor 1, putative / 0.715
2j5x GSPADP-ribosylation factor 6 / 0.714
5d3q GDPDynamin-1 3.6.5.5 0.714
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.713
3r9i ADPSeptum site-determining protein MinD / 0.712
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.711
1gwn GTPRho-related GTP-binding protein RhoE / 0.710
4e07 ACPPlasmid partitioning protein ParF / 0.710
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.709
1yu9 GNPRas-related protein Rab-4A / 0.709
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.709
3x1z GNPRas-related protein Rap-1b / 0.707
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.707
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.707
4yqf GDPSeptin-9 / 0.707
3k3b ADPKinesin-like protein KIF11 / 0.706
3q5d GDPAtlastin-1 3.6.5 0.706
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.706
3eg5 GNPCell division control protein 42 homolog / 0.703
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.702
3kkq GDPRas-related protein M-Ras / 0.702
4l8g GDPGTPase KRas / 0.702
4l9s GDPGTPase HRas / 0.701
4luc GDPGTPase KRas / 0.700
2iut AGSDNA translocase FtsK / 0.699
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.699
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.698
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
4epx GDPGTPase KRas / 0.698
5aun ADPIron-sulfur cluster carrier protein / 0.698
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.696
3oes GNPGTPase RhebL1 / 0.696
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.695
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.692
4dzz ADPPlasmid partitioning protein ParF / 0.692
1sxj AGSReplication factor C subunit 1 / 0.691
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.691
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.691
5bn3 ADPV-type ATP synthase alpha chain / 0.689
5bn3 ADPNEQ263 / 0.689
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.687
2vf7 ADPUvrABC system protein A / 0.687
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.686
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.685
3mjh GTPRas-related protein Rab-5A / 0.685
2g1q ADPKinesin-like protein KIF11 / 0.684
1e4v AP5Adenylate kinase / 0.683
2uyi ADPKinesin-like protein KIF11 / 0.683
3nbx ADPATPase RavA 3.6.3 0.683
1ank ANPAdenylate kinase / 0.682
1svw GTPProbable GTP-binding protein EngB / 0.682
4hse ADPChaperone protein ClpB / 0.682
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.682
1rrg GDPADP-ribosylation factor 1 / 0.681
1yrs ADPKinesin-like protein KIF11 / 0.681
2zr9 DTPProtein RecA / 0.679
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.679
4o25 GTPGTP-binding protein Rheb / 0.679
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.678
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.678
4l16 ADPFidgetin-like protein 1 3.6.4 0.678
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.678
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.677
5c46 GSPRas-related protein Rab-11A / 0.677
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.676
3tqc ADPPantothenate kinase / 0.675
2c96 ATPPsp operon transcriptional activator / 0.673
4mit GTPRho-related protein racC / 0.673
3m0e ATPTranscriptional regulator (NtrC family) / 0.671
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.671
5da9 AGSUncharacterized protein / 0.671
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.670
5itz GTPTubulin alpha-1B chain / 0.670
1fnn ADPORC1-type DNA replication protein / 0.669
3kz1 GSPTransforming protein RhoA / 0.668
1ii6 ADPKinesin-like protein KIF11 / 0.667
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.667
3ddc GNPGTPase HRas / 0.667
2r9v ATPATP synthase subunit alpha / 0.666
4jlb ADPAdenylate kinase / 0.666
1dvr ATFAdenylate kinase / 0.665
3vth APCCarbamoyltransferase / 0.665
1z6t ADPApoptotic protease-activating factor 1 / 0.664
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.664
4d0l GSPRas-related protein Rab-11A / 0.664
4oi2 ADPProtein clpf-1 / 0.664
1tf7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.663
1u9i ATPCircadian clock protein kinase KaiC 2.7.11.1 0.663
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.663
3hpq AP5Adenylate kinase / 0.663
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.662
2c9o ADPRuvB-like 1 3.6.4.12 0.662
2r5t ANPSerine/threonine-protein kinase Sgk1 2.7.11.1 0.662
3ref GDPRho family GTPase / 0.661
3ryh GTPTubulin alpha chain / 0.661
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
2vp0 TTPDeoxynucleoside kinase / 0.660
5dac AGSUncharacterized protein / 0.660
5di3 GNPADP-ribosylation factor-like protein 3 / 0.660
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.659
2hld ANPATP synthase subunit alpha, mitochondrial / 0.658
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
4fvq ATPTyrosine-protein kinase JAK2 / 0.657
1sq5 ADPPantothenate kinase 2.7.1.33 0.656
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.656
4o2l GTPGTP-binding protein Rheb / 0.656
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.655
1d5c GDPGTPase (Rab6) / 0.653
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.653
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.653
4a1z ADPKinesin-like protein KIF11 / 0.653
4iij GTPTubulin alpha-1B chain / 0.653
4qos ADPPsp operon transcriptional activator / 0.653
4jl5 ADPAdenylate kinase / 0.652
4jl8 ADPAdenylate kinase / 0.652
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.652
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.651
4ihq ADPConserved Archaeal protein / 0.651
1zbd GTPRas-related protein Rab-3A / 0.650
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.650
4aza MGOEukaryotic translation initiation factor 4E / 0.650