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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
2zro ADP Protein RecA

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2zro ADPProtein RecA / 1.061
1xp8 AGSProtein RecA / 0.875
1xmv ADPProtein RecA / 0.847
2zrj AGSProtein RecA / 0.847
2zr9 DTPProtein RecA / 0.762
3ieu GDPGTPase Era / 0.757
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.752
4lrw GDPGTPase KRas / 0.752
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.750
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.749
3r9i ADPSeptum site-determining protein MinD / 0.748
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.747
3ea5 GDPGTP-binding nuclear protein Ran / 0.747
3l9h ADPKinesin-like protein KIF11 / 0.747
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.744
4b7b ADPKinesin-like protein KIF11 / 0.744
2whx ADPGenome polyprotein 3.4.21.91 0.742
2x2r ADPKinesin-like protein KIF11 / 0.742
5cyo GDPSeptin-9 / 0.742
2pg2 ADPKinesin-like protein KIF11 / 0.741
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.741
3d8b ADPFidgetin-like protein 1 3.6.4 0.740
2uyi ADPKinesin-like protein KIF11 / 0.737
1b7t ADPMyosin heavy chain, striated muscle / 0.736
1yrs ADPKinesin-like protein KIF11 / 0.729
3t1t GDPProbable gliding protein mglA / 0.728
4dsu GDPGTPase KRas / 0.727
1sdm ADPKinesin heavy chain-like protein / 0.726
4hi0 GDPUrease accessory protein UreG / 0.726
4luc GDPGTPase KRas / 0.725
2zfi ADPKinesin-like protein KIF1A / 0.724
3cob ADPKinesin heavy chain-like protein / 0.724
4l8g GDPGTPase KRas / 0.723
4l9s GDPGTPase HRas / 0.720
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.718
2zre AGSProtein RecA / 0.717
4a1z ADPKinesin-like protein KIF11 / 0.717
4wa7 GDPGTPase KRas / 0.717
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.716
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.716
4a51 ADPKinesin-like protein KIF11 / 0.716
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.716
2x7e ADPKinesin-like protein KIF11 / 0.715
3l1c ADPProtein claret segregational / 0.715
4ncl GDPEukaryotic translation initiation factor 5B / 0.714
4pjk ADPMyosin-2 heavy chain / 0.714
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.714
5bn3 ADPV-type ATP synthase alpha chain / 0.714
5bn3 ADPNEQ263 / 0.714
1g16 GDPRas-related protein SEC4 / 0.713
4epw GDPGTPase KRas / 0.713
4lv6 GDPGTPase KRas / 0.713
1z0a GDPRas-related protein Rab-2A / 0.710
3tkl GTPRas-related protein Rab-1A / 0.710
4yqf GDPSeptin-9 / 0.709
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.708
5aun ADPIron-sulfur cluster carrier protein / 0.707
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.705
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.705
3c41 ANPAmino acid ABC transporter / 0.705
4lpk GDPGTPase KRas / 0.705
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.704
3w3z GTPGTP-binding nuclear protein Ran / 0.702
4jky ADPAdenylate kinase / 0.702
1t91 GTPRas-related protein Rab-7a / 0.701
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.701
3tlx ADPAdenylate kinase 2 / 0.701
4d81 ADPAAA ATPase, central domain protein / 0.700
4a28 ADPKinesin-like protein KIF11 / 0.699
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.698
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.697
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.697
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.697
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.697
3tjz GNPADP-ribosylation factor 1 / 0.697
4g01 GDPRas-related protein RABF2b / 0.697
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.696
3qbv GDPCell division control protein 42 homolog / 0.696
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.696
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.694
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.694
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.694
3tqc ADPPantothenate kinase / 0.694
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.693
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.693
1g6o ADPCag alpha / 0.693
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.693
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.693
1wbb ADPDNA mismatch repair protein MutS / 0.692
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.692
2fna ADPUncharacterized protein / 0.692
4cf7 ADPAdenylate kinase / 0.692
3kuc GDPRas-related protein Rap-1A / 0.691
2ce2 GDPGTPase HRas / 0.690
3kud GDPGTPase HRas / 0.690
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.689
3myk ANPMyosin-2 heavy chain / 0.689
4pjj ADPUnconventional myosin-VI / 0.689
1nly AGSCag alpha / 0.688
1n6m ADPProtein claret segregational / 0.687
2fl2 ADPKinesin-like protein KIF11 / 0.687
2y65 ADPKinesin heavy chain / 0.687
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.687
1d5c GDPGTPase (Rab6) / 0.686
1jx2 ADPMyosin-2 heavy chain / 0.686
3mjh GTPRas-related protein Rab-5A / 0.686
1kmq GNPTransforming protein RhoA / 0.684
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.684
3q5d GDPAtlastin-1 3.6.5 0.684
1xms ANPProtein RecA / 0.683
1z0d GDPRas-related protein Rab-5C / 0.683
4itr GDPCell division control protein 42 homolog / 0.683
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.682
1sq5 ADPPantothenate kinase 2.7.1.33 0.682
2cls GTPRho-related GTP-binding protein Rho6 / 0.682
2q3f GNPRas-related GTP-binding protein D / 0.682
3cph GDPRas-related protein SEC4 / 0.682
5fl3 ADPPili retraction protein PilT / 0.682
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.681
2ncd ADPProtein claret segregational / 0.681
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.681
1xtr GNPGTP-binding protein Rheb / 0.680
3ref GDPRho family GTPase / 0.680
4jl6 ADPAdenylate kinase / 0.680
3law GNPRas-related protein Rab-7a / 0.679
4jlo ADPAdenylate kinase / 0.679
4obe GDPGTPase KRas / 0.679
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.678
3pcr GTPADP-ribosylation factor 6 / 0.678
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.677
1x1r GDPRas-related protein M-Ras / 0.677
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.677
4xoi GTPTransforming protein RhoA / 0.677
1ky2 GNPGTP-binding protein YPT7 / 0.676
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.676
3kkq GDPRas-related protein M-Ras / 0.676
3zia ATPATP synthase subunit alpha, mitochondrial / 0.676
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.675
3tgp GNPGTPase HRas / 0.675
4asu ADPATP synthase subunit alpha, mitochondrial / 0.675
4iei ADPGene 2 protein / 0.675
4o2r GDPGTP-binding protein Rheb / 0.675
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.674
4dzz ADPPlasmid partitioning protein ParF / 0.674
4q03 GDPGTPase KRas / 0.674
4goj GNPADP-ribosylation factor-like protein 3 / 0.673
4q02 GDPGTPase KRas / 0.673
1z2a GDPRas-related protein Rab-23 / 0.672
3k1j ADPATP-dependent protease Lon / 0.672
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.672
3x1w GDPRas-related protein Rap-1b / 0.672
4uj3 GNPRas-related protein Rab-11A / 0.672
4xsg GSPTransforming protein RhoA / 0.672
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.671
4ihq ADPConserved Archaeal protein / 0.671
4xvq GNPGTPase HRas / 0.671
4y0v GDPADP-ribosylation factor 1, putative / 0.671
1s1c GNPTransforming protein RhoA / 0.670
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.670
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.670
4idp GNPAtlastin-1 3.6.5 0.670
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.669
4dls GNPGTPase HRas / 0.669
1z0f GDPRas-related protein Rab-14 / 0.668
4gp6 ADPMetallophosphoesterase / 0.668
2iut AGSDNA translocase FtsK / 0.667
3eg5 GNPCell division control protein 42 homolog / 0.667
4ike ADPAdenylate kinase / 0.667
4ylg GDPADP-ribosylation factor 1, putative / 0.667
1yzq GNPRas-related protein Rab-6A / 0.666
4ap0 ADPKinesin-like protein KIF11 / 0.666
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.665
2qen ADPWalker-Type ATPase / 0.664
4iok ADPFormate--tetrahydrofolate ligase / 0.664
1rrg GDPADP-ribosylation factor 1 / 0.663
2rgg GNPGTPase HRas / 0.663
3b1x GNPFerrous iron transport protein B / 0.663
4dso GSPGTPase KRas / 0.663
4jl5 ADPAdenylate kinase / 0.663
4qnr ATPPsp operon transcriptional activator / 0.663
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.663
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.662
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.662
3k9l GNPGTPase HRas / 0.661
3qbt GNPRas-related protein Rab-8A / 0.661
1l8q ADPChromosomal replication initiator protein DnaA / 0.660
2gm1 ADPKinesin-like protein KIF11 / 0.660
1am4 GNPCell division control protein 42 homolog / 0.659
1svl ADPLarge T antigen 3.6.4 0.659
4o2l GTPGTP-binding protein Rheb / 0.659
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.658
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.658
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.658
1yra GDPGPN-loop GTPase PAB0955 / 0.658
2o8b ADPDNA mismatch repair protein Msh2 / 0.658
3e5h GNPRas-related protein Rab-28 / 0.658
4idn GNPAtlastin-1 3.6.5 0.658
2fg5 GNPRas-related protein Rab-31 / 0.657
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.657
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.656
2xae ADPKinesin-like protein KIF11 / 0.656
2zsa ADPPantothenate kinase 2.7.1.33 0.656
4i1v ADPDephospho-CoA kinase / 0.656
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.655
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.655
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.655
1z6t ADPApoptotic protease-activating factor 1 / 0.654
2fe4 GDPRas-related protein Rab-6B / 0.654
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.654
3thy ADPDNA mismatch repair protein Msh2 / 0.654
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.653
4js0 GNPCell division control protein 42 homolog / 0.653
1g17 GNPRas-related protein SEC4 / 0.652
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.652
1lfd GNPGTPase HRas / 0.652
2oap ANPType II secretion system protein (GspE-2) / 0.650