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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
2xsz ATP RuvB-like 2 3.6.4.12

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2xsz ATPRuvB-like 2 3.6.4.12 1.104
2c9o ADPRuvB-like 1 3.6.4.12 0.897
3uk6 ADPRuvB-like 2 3.6.4.12 0.877
4ww4 ADPRuvB-like helicase / 0.866
4hse ADPChaperone protein ClpB / 0.802
1fnn ADPORC1-type DNA replication protein / 0.801
1l8q ADPChromosomal replication initiator protein DnaA / 0.799
1w5s ADPORC1-type DNA replication protein 2 / 0.794
2gm1 ADPKinesin-like protein KIF11 / 0.792
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.782
3k1j ADPATP-dependent protease Lon / 0.775
4b7b ADPKinesin-like protein KIF11 / 0.775
2y65 ADPKinesin heavy chain / 0.761
2ql6 ADPNicotinamide riboside kinase 1 / 0.760
1w5t ADPORC1-type DNA replication protein 2 / 0.751
4qbi AP5Adenylate kinase / 0.750
5fl3 ADPPili retraction protein PilT / 0.749
2pg2 ADPKinesin-like protein KIF11 / 0.746
4dxa GSPRas-related protein Rap-1b / 0.746
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.745
1z0a GDPRas-related protein Rab-2A / 0.745
4kvg GTPRas-related protein Rap-1A / 0.744
2ffq GSPRas-related protein Rab-6B / 0.742
4dso GSPGTPase KRas / 0.742
1fmw ATPMyosin-2 heavy chain / 0.741
3l9h ADPKinesin-like protein KIF11 / 0.740
1z0f GDPRas-related protein Rab-14 / 0.736
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.736
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.736
3ieu GDPGTPase Era / 0.736
3kuc GDPRas-related protein Rap-1A / 0.736
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.735
1p3j AP5Adenylate kinase / 0.734
4lpk GDPGTPase KRas / 0.734
4o25 GTPGTP-binding protein Rheb / 0.734
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.733
4qbh AP5Adenylate kinase / 0.733
4ql3 GDPGTPase KRas / 0.733
3kkq GDPRas-related protein M-Ras / 0.732
4q03 GDPGTPase KRas / 0.732
4wa7 GDPGTPase KRas / 0.732
5fm6 ADPRuvB-like helicase / 0.732
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.731
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.731
4xsg GSPTransforming protein RhoA / 0.731
2ce2 GDPGTPase HRas / 0.730
2gil GTPRas-related protein Rab-6A / 0.730
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.728
2fna ADPUncharacterized protein / 0.727
4obe GDPGTPase KRas / 0.727
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.727
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.726
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.725
3q5d GDPAtlastin-1 3.6.5 0.725
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.724
2eck ADPAdenylate kinase / 0.723
2xae ADPKinesin-like protein KIF11 / 0.723
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.722
3t1t GDPProbable gliding protein mglA / 0.721
1z0d GDPRas-related protein Rab-5C / 0.720
1a2b GSPTransforming protein RhoA / 0.719
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.719
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.719
1jx2 ADPMyosin-2 heavy chain / 0.718
1sdm ADPKinesin heavy chain-like protein / 0.718
2c9c ATPPsp operon transcriptional activator / 0.718
4epw GDPGTPase KRas / 0.718
2q2z ADPKinesin-like protein KIF11 / 0.717
3x1w GDPRas-related protein Rap-1b / 0.717
4lv6 GDPGTPase KRas / 0.717
4tq9 GDPGTPase KRas / 0.716
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.715
1x1r GDPRas-related protein M-Ras / 0.715
4ldj GDPGTPase KRas / 0.715
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.714
3m0e ATPTranscriptional regulator (NtrC family) / 0.714
3tlx ADPAdenylate kinase 2 / 0.714
1d5c GDPGTPase (Rab6) / 0.713
2dft ADPShikimate kinase 2.7.1.71 0.713
4cf7 ADPAdenylate kinase / 0.713
4qbg AP5Adenylate kinase / 0.713
2c96 ATPPsp operon transcriptional activator / 0.712
3tgp GNPGTPase HRas / 0.712
4lj7 MNTChaperone protein ClpB / 0.712
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.710
4dsu GDPGTPase KRas / 0.710
5aun ADPIron-sulfur cluster carrier protein / 0.710
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.709
3cph GDPRas-related protein SEC4 / 0.709
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.708
3kud GDPGTPase HRas / 0.707
5fm7 ADPRuvB-like helicase / 0.707
2zfi ADPKinesin-like protein KIF1A / 0.706
4ap0 ADPKinesin-like protein KIF11 / 0.705
4q02 GDPGTPase KRas / 0.705
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.705
1zbd GTPRas-related protein Rab-3A / 0.704
3tqc ADPPantothenate kinase / 0.704
1uad GNPRas-related protein Ral-A / 0.703
3cob ADPKinesin heavy chain-like protein / 0.703
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.703
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.702
1oix GDPRas-related protein Rab-11A / 0.702
2j5x GSPADP-ribosylation factor 6 / 0.702
1xmv ADPProtein RecA / 0.701
2g1q ADPKinesin-like protein KIF11 / 0.701
4ncl GDPEukaryotic translation initiation factor 5B / 0.701
1m7b GTPRho-related GTP-binding protein RhoE / 0.700
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.700
3tkl GTPRas-related protein Rab-1A / 0.700
3wyf GTPGTP-binding nuclear protein / 0.700
4x8o AP5Adenylate kinase / 0.700
4ylg GDPADP-ribosylation factor 1, putative / 0.700
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.699
4itr GDPCell division control protein 42 homolog / 0.699
4zca ADPKinesin-like protein KIF11 / 0.699
4d81 ADPAAA ATPase, central domain protein / 0.698
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.697
4epx GDPGTPase KRas / 0.697
1lfd GNPGTPase HRas / 0.696
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.694
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.694
4jky ADPAdenylate kinase / 0.694
4l8g GDPGTPase KRas / 0.693
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.692
1ii6 ADPKinesin-like protein KIF11 / 0.691
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.691
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.690
3k3b ADPKinesin-like protein KIF11 / 0.690
4g0n GNPGTPase HRas / 0.689
4l9s GDPGTPase HRas / 0.689
4mkh AP5Adenylate kinase / 0.689
1mma ADPMyosin-2 heavy chain / 0.688
1yra GDPGPN-loop GTPase PAB0955 / 0.688
2fe4 GDPRas-related protein Rab-6B / 0.688
4cym GCPRas-related protein Rab-32 / 0.688
4hi0 GDPUrease accessory protein UreG / 0.688
4mkf AP5Adenylate kinase / 0.687
4pjk ADPMyosin-2 heavy chain / 0.687
2bku GTPGTP-binding nuclear protein Ran / 0.686
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.686
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.686
2gcp GSPRho-related GTP-binding protein RhoC / 0.685
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.685
2zrj AGSProtein RecA / 0.685
4a51 ADPKinesin-like protein KIF11 / 0.685
4lrw GDPGTPase KRas / 0.685
2rgx AP5Adenylate kinase / 0.684
4qm6 GTPMetallophosphoesterase / 0.684
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.683
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.683
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.683
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.683
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.682
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.682
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.682
4xvr GNPGTPase HRas / 0.682
1svl ADPLarge T antigen 3.6.4 0.681
1svm ATPLarge T antigen 3.6.4 0.681
2qaj AP5Adenylate kinase / 0.681
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.681
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.681
4xvq GNPGTPase HRas / 0.681
5ftc ADPTPR domain protein / 0.680
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
3k8y GNPGTPase HRas / 0.679
4o2l GTPGTP-binding protein Rheb / 0.679
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.678
3ea0 ATPATPase, ParA family / 0.678
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.678
3thy ADPDNA mismatch repair protein Msh2 / 0.678
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.678
4idn GNPAtlastin-1 3.6.5 0.678
4jl5 ADPAdenylate kinase / 0.678
1wdt GTPElongation factor G (EF-G-2) / 0.677
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.677
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.677
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.677
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.677
4iei ADPGene 2 protein / 0.677
1g6o ADPCag alpha / 0.676
3pcr GTPADP-ribosylation factor 6 / 0.676
4dvg GSPRho family GTPase / 0.676
4iok ADPFormate--tetrahydrofolate ligase / 0.676
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.675
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.675
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.675
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.675
4luc GDPGTPase KRas / 0.674
1cxz GSPTransforming protein RhoA / 0.673
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.673
1am4 GNPCell division control protein 42 homolog / 0.672
4jjz ADPFormate--tetrahydrofolate ligase / 0.672
1gwn GTPRho-related GTP-binding protein RhoE / 0.670
2ewv ADPTwitching motility protein PilT / 0.670
4a1z ADPKinesin-like protein KIF11 / 0.670
4ys0 ADPProtein translocase subunit SecA / 0.670
1sq5 ADPPantothenate kinase 2.7.1.33 0.669
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.669
4qxa GTPRas-related protein Rab-9A / 0.669
1xtr GNPGTP-binding protein Rheb / 0.668
5bn3 ADPV-type ATP synthase alpha chain / 0.668
5bn3 ADPNEQ263 / 0.668
3a6p GTPGTP-binding nuclear protein Ran / 0.667
3nbx ADPATPase RavA 3.6.3 0.667
4qnr ATPPsp operon transcriptional activator / 0.667
1kmq GNPTransforming protein RhoA / 0.666
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.666
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.666
4v02 ATPSite-determining protein / 0.666
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.665
1b7t ADPMyosin heavy chain, striated muscle / 0.664
2cls GTPRho-related GTP-binding protein Rho6 / 0.664
3mjh GTPRas-related protein Rab-5A / 0.664
4a28 ADPKinesin-like protein KIF11 / 0.664
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.663
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.663
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.663
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.662
4pfp ADPUnconventional myosin-VI / 0.662
4db1 ANPMyosin-7 / 0.661
1a4r GNHCell division control protein 42 homolog / 0.660
1n6m ADPProtein claret segregational / 0.660
2zet GTPRas-related protein Rab-27B / 0.660
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.660
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.659
2d7d ADPUvrABC system protein B / 0.659
4hdq GNPRas-related protein Rap-1b / 0.659
4uj3 GNPRas-related protein Rab-11A / 0.659
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.658
2rgg GNPGTPase HRas / 0.658
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.657
1xjq ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.657
4g01 GDPRas-related protein RABF2b / 0.657
1xts GTPGTP-binding protein Rheb / 0.656
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.656
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.656
4d0l GSPRas-related protein Rab-11A / 0.656
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.655
1zc3 GNPRas-related protein Ral-A / 0.654
3w3z GTPGTP-binding nuclear protein Ran / 0.654
4dls GNPGTPase HRas / 0.654
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.653
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.653
4hdo GNPRas-related protein Rap-1b / 0.653
4oi2 ADPProtein clpf-1 / 0.653
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
1e4v AP5Adenylate kinase / 0.652
2h12 CMXCitrate synthase / 0.652
1ky2 GNPGTP-binding protein YPT7 / 0.651
2x2r ADPKinesin-like protein KIF11 / 0.651
3l1c ADPProtein claret segregational / 0.651
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.651
1w5t ANPORC1-type DNA replication protein 2 / 0.650
1yu9 GNPRas-related protein Rab-4A / 0.650