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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
5bn4 ANP V-type ATP synthase alpha chain

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5bn4 ANPV-type ATP synthase alpha chain / 0.990
5bn3 ADPV-type ATP synthase alpha chain / 0.901
5bn3 ADPNEQ263 / 0.901
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.774
1b7t ADPMyosin heavy chain, striated muscle / 0.748
2o8b ADPDNA mismatch repair protein Msh2 / 0.744
3tqc ADPPantothenate kinase / 0.742
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.739
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.739
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.738
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.738
4cf7 ADPAdenylate kinase / 0.725
3kz1 GSPTransforming protein RhoA / 0.723
4lhv GDPRas-related protein Rab-8A / 0.722
5aun ADPIron-sulfur cluster carrier protein / 0.722
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.719
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.719
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.719
1z0a GDPRas-related protein Rab-2A / 0.717
4pk4 ADPUnconventional myosin-VI / 0.716
2y65 ADPKinesin heavy chain / 0.715
1z0f GDPRas-related protein Rab-14 / 0.714
4jsy GTPMetallophosphoesterase / 0.714
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.713
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.713
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.712
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.712
1g16 GDPRas-related protein SEC4 / 0.711
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.710
1wbb ADPDNA mismatch repair protein MutS / 0.709
3cph GDPRas-related protein SEC4 / 0.709
3ea5 GDPGTP-binding nuclear protein Ran / 0.707
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.706
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.706
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.706
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.706
3q5d GDPAtlastin-1 3.6.5 0.705
4jld ADPAdenylate kinase / 0.704
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.703
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.702
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.698
1sq5 ADPPantothenate kinase 2.7.1.33 0.698
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.696
4xsg GSPTransforming protein RhoA / 0.695
4d81 ADPAAA ATPase, central domain protein / 0.694
4lpk GDPGTPase KRas / 0.693
4obe GDPGTPase KRas / 0.693
2rgx AP5Adenylate kinase / 0.692
3kud GDPGTPase HRas / 0.692
4itr GDPCell division control protein 42 homolog / 0.690
4o3m ADPBloom syndrome protein 3.6.4.12 0.690
2fna ADPUncharacterized protein / 0.689
3k1j ADPATP-dependent protease Lon / 0.689
3kkq GDPRas-related protein M-Ras / 0.689
1zbd GTPRas-related protein Rab-3A / 0.688
2cls GTPRho-related GTP-binding protein Rho6 / 0.688
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
4dsu GDPGTPase KRas / 0.688
1d5c GDPGTPase (Rab6) / 0.687
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.687
3d8b ADPFidgetin-like protein 1 3.6.4 0.686
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.684
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.683
1ny5 ADPTranscriptional regulator (NtrC family) / 0.682
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.682
2iut AGSDNA translocase FtsK / 0.681
4luc GDPGTPase KRas / 0.681
4pfp ADPUnconventional myosin-VI / 0.681
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.680
2qen ADPWalker-Type ATPase / 0.680
3vhx GTPADP-ribosylation factor 6 / 0.680
5c46 GSPRas-related protein Rab-11A / 0.679
4qbh AP5Adenylate kinase / 0.678
1svl ADPLarge T antigen 3.6.4 0.677
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.676
3a6p GTPGTP-binding nuclear protein Ran / 0.675
4l9s GDPGTPase HRas / 0.675
4tyq AP5Adenylate kinase / 0.675
2bku GTPGTP-binding nuclear protein Ran / 0.674
2gm1 ADPKinesin-like protein KIF11 / 0.674
2whx ADPGenome polyprotein 3.4.21.91 0.674
2zts ADPUncharacterized protein / 0.674
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.674
4lrw GDPGTPase KRas / 0.674
4q02 GDPGTPase KRas / 0.674
4q03 GDPGTPase KRas / 0.674
4epx GDPGTPase KRas / 0.673
4qbi AP5Adenylate kinase / 0.672
1nbm ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
2fe4 GDPRas-related protein Rab-6B / 0.669
2j5x GSPADP-ribosylation factor 6 / 0.669
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.669
3w3z GTPGTP-binding nuclear protein Ran / 0.669
4k81 GTPGTPase HRas / 0.669
1a4r GNHCell division control protein 42 homolog / 0.668
1z2a GDPRas-related protein Rab-23 / 0.667
3q9l ATPSeptum site-determining protein MinD / 0.665
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.665
3ref GDPRho family GTPase / 0.664
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.663
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.662
1w7i ADPUnconventional myosin-Va / 0.661
3tnf GNPRas-related protein Rab-8A / 0.661
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.661
1rrg GDPADP-ribosylation factor 1 / 0.660
3x1w GDPRas-related protein Rap-1b / 0.659
4oi2 ADPProtein clpf-1 / 0.659
1jx2 ADPMyosin-2 heavy chain / 0.658
1x1r GDPRas-related protein M-Ras / 0.658
4lv6 GDPGTPase KRas / 0.658
4tq9 GDPGTPase KRas / 0.658
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.657
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.657
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.657
3t1t GDPProbable gliding protein mglA / 0.657
4o2r GDPGTP-binding protein Rheb / 0.657
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.656
4ldj GDPGTPase KRas / 0.656
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.655
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.655
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.654
3qbv GDPCell division control protein 42 homolog / 0.654
3zia ATPATP synthase subunit alpha, mitochondrial / 0.654
4hse ADPChaperone protein ClpB / 0.654
1cxz GSPTransforming protein RhoA / 0.653
1p9w ANPType II secretion system protein E / 0.653
1sdm ADPKinesin heavy chain-like protein / 0.653
4y0v GDPADP-ribosylation factor 1, putative / 0.653
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.651
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.651
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.650
4dq1 UMPThymidylate synthase / 0.650
4jl6 ADPAdenylate kinase / 0.650