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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
3nbx ADP ATPase RavA 3.6.3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3nbx ADPATPase RavA 3.6.3 1.047
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.778
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.764
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.745
3k1j ADPATP-dependent protease Lon / 0.744
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.740
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.737
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.733
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.730
1z0a GDPRas-related protein Rab-2A / 0.730
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.725
4o25 GTPGTP-binding protein Rheb / 0.725
1z0f GDPRas-related protein Rab-14 / 0.723
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.720
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.720
2xae ADPKinesin-like protein KIF11 / 0.719
4l16 ADPFidgetin-like protein 1 3.6.4 0.719
2c96 ATPPsp operon transcriptional activator / 0.718
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.718
3uk6 ADPRuvB-like 2 3.6.4.12 0.718
2hld ANPATP synthase subunit alpha, mitochondrial / 0.716
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.716
4hi0 GDPUrease accessory protein UreG / 0.716
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.713
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.713
4d0l GSPRas-related protein Rab-11A / 0.713
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.712
2x2r ADPKinesin-like protein KIF11 / 0.712
2uyi ADPKinesin-like protein KIF11 / 0.711
5c46 GSPRas-related protein Rab-11A / 0.710
1fmw ATPMyosin-2 heavy chain / 0.709
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.707
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.707
4b7b ADPKinesin-like protein KIF11 / 0.707
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.706
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.706
3mjh GTPRas-related protein Rab-5A / 0.706
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.705
4a51 ADPKinesin-like protein KIF11 / 0.705
4dsu GDPGTPase KRas / 0.703
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.703
3kuc GDPRas-related protein Rap-1A / 0.701
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.701
2fl2 ADPKinesin-like protein KIF11 / 0.699
4ldj GDPGTPase KRas / 0.698
1am4 GNPCell division control protein 42 homolog / 0.697
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.697
2ce2 GDPGTPase HRas / 0.697
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.697
3cob ADPKinesin heavy chain-like protein / 0.697
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.697
1zbd GTPRas-related protein Rab-3A / 0.696
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.696
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.694
4lpk GDPGTPase KRas / 0.694
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.693
2cl6 CAGGTPase HRas / 0.693
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.693
1ii6 ADPKinesin-like protein KIF11 / 0.690
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.690
4d81 ADPAAA ATPase, central domain protein / 0.690
4ww4 ADPRuvB-like helicase / 0.690
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.689
2gil GTPRas-related protein Rab-6A / 0.689
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.689
2rgx AP5Adenylate kinase / 0.689
4l8g GDPGTPase KRas / 0.689
4l9s GDPGTPase HRas / 0.689
4lrw GDPGTPase KRas / 0.689
4ncl GDPEukaryotic translation initiation factor 5B / 0.689
1jx2 ADPMyosin-2 heavy chain / 0.688
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.687
2bku GTPGTP-binding nuclear protein Ran / 0.687
3kkq GDPRas-related protein M-Ras / 0.687
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.687
4iei ADPGene 2 protein / 0.687
4pjj ADPUnconventional myosin-VI / 0.687
4epw GDPGTPase KRas / 0.686
4q02 GDPGTPase KRas / 0.686
1m7b GTPRho-related GTP-binding protein RhoE / 0.685
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.685
4lv6 GDPGTPase KRas / 0.685
4qnr ATPPsp operon transcriptional activator / 0.685
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.684
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
2c9c ATPPsp operon transcriptional activator / 0.684
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.684
4q03 GDPGTPase KRas / 0.684
4xsg GSPTransforming protein RhoA / 0.684
5fl3 ADPPili retraction protein PilT / 0.684
1sq5 ADPPantothenate kinase 2.7.1.33 0.683
2l0x GDPGTP-binding protein Rheb / 0.683
2osb AP5Adenylate kinase / 0.683
3tkl GTPRas-related protein Rab-1A / 0.683
1w5t ANPORC1-type DNA replication protein 2 / 0.682
3kz1 GSPTransforming protein RhoA / 0.682
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.682
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.681
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.681
3d8b ADPFidgetin-like protein 1 3.6.4 0.681
3m0e ATPTranscriptional regulator (NtrC family) / 0.681
4dso GSPGTPase KRas / 0.681
3kud GDPGTPase HRas / 0.680
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.679
1t91 GTPRas-related protein Rab-7a / 0.679
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.678
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.678
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.677
2vf7 ADPUvrABC system protein A / 0.677
2zet GTPRas-related protein Rab-27B / 0.677
4xvq GNPGTPase HRas / 0.677
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.674
5dif GNPGTP-binding nuclear protein Ran / 0.674
1yrs ADPKinesin-like protein KIF11 / 0.673
3a6p GTPGTP-binding nuclear protein Ran / 0.673
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.673
4lhv GDPRas-related protein Rab-8A / 0.673
2iut AGSDNA translocase FtsK / 0.672
3q5d GDPAtlastin-1 3.6.5 0.672
4pfp ADPUnconventional myosin-VI / 0.672
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.671
3l9h ADPKinesin-like protein KIF11 / 0.671
1w7i ADPUnconventional myosin-Va / 0.670
2pg2 ADPKinesin-like protein KIF11 / 0.670
2zts ADPUncharacterized protein / 0.670
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.669
3pcr GTPADP-ribosylation factor 6 / 0.669
4luc GDPGTPase KRas / 0.669
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.668
2gcp GSPRho-related GTP-binding protein RhoC / 0.667
2xsz ATPRuvB-like 2 3.6.4.12 0.667
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.667
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.667
4xoi GTPTransforming protein RhoA / 0.667
1cxz GSPTransforming protein RhoA / 0.666
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.666
1xts GTPGTP-binding protein Rheb / 0.665
2zfi ADPKinesin-like protein KIF1A / 0.665
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.665
1g16 GDPRas-related protein SEC4 / 0.664
3k9l GNPGTPase HRas / 0.664
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.664
4idn GNPAtlastin-1 3.6.5 0.664
4iok ADPFormate--tetrahydrofolate ligase / 0.664
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.663
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.663
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.662
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.662
4obe GDPGTPase KRas / 0.662
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.661
1gwn GTPRho-related GTP-binding protein RhoE / 0.660
1ny5 ADPTranscriptional regulator (NtrC family) / 0.659
1oix GDPRas-related protein Rab-11A / 0.659
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.659
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.659
3x1w GDPRas-related protein Rap-1b / 0.659
4hse ADPChaperone protein ClpB / 0.659
4ql3 GDPGTPase KRas / 0.659
4tq9 GDPGTPase KRas / 0.659
4xvu ATPATPase GET3 / 0.659
5d3q GDPDynamin-1 3.6.5.5 0.659
1xmv ADPProtein RecA / 0.658
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.658
3r9i ADPSeptum site-determining protein MinD / 0.658
4epx GDPGTPase KRas / 0.658
4pjk ADPMyosin-2 heavy chain / 0.658
4wa7 GDPGTPase KRas / 0.658
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.656
3cph GDPRas-related protein SEC4 / 0.656
3l1c ADPProtein claret segregational / 0.656
4jky ADPAdenylate kinase / 0.656
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.655
1mab ATPATP synthase subunit alpha, mitochondrial / 0.654
2cls GTPRho-related GTP-binding protein Rho6 / 0.654
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.654
3oee ANPATP synthase subunit alpha, mitochondrial / 0.654
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.654
4kod ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.654
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.653
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.653
1svl ADPLarge T antigen 3.6.4 0.652
2zrj AGSProtein RecA / 0.652
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.651
2zs9 ADPPantothenate kinase 2.7.1.33 0.651
4k81 GTPGTPase HRas / 0.651
1f5n GNPGuanylate-binding protein 1 / 0.650
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.650