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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
2ce7 ADP ATP-dependent zinc metalloprotease FtsH

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 1.114
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.833
4d81 ADPAAA ATPase, central domain protein / 0.798
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.785
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.785
2pg2 ADPKinesin-like protein KIF11 / 0.782
2xae ADPKinesin-like protein KIF11 / 0.780
2uyi ADPKinesin-like protein KIF11 / 0.778
2zrj AGSProtein RecA / 0.776
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.772
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.770
4b7b ADPKinesin-like protein KIF11 / 0.768
3l9h ADPKinesin-like protein KIF11 / 0.767
2fl2 ADPKinesin-like protein KIF11 / 0.766
4lrw GDPGTPase KRas / 0.766
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.766
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.765
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.762
2x7e ADPKinesin-like protein KIF11 / 0.761
1sdm ADPKinesin heavy chain-like protein / 0.760
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.759
4obe GDPGTPase KRas / 0.756
5cyo GDPSeptin-9 / 0.753
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.751
1yrs ADPKinesin-like protein KIF11 / 0.750
3d8b ADPFidgetin-like protein 1 3.6.4 0.750
4ncl GDPEukaryotic translation initiation factor 5B / 0.750
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.749
3k1j ADPATP-dependent protease Lon / 0.748
2zfi ADPKinesin-like protein KIF1A / 0.746
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.746
3ieu GDPGTPase Era / 0.745
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.743
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.742
3qbv GDPCell division control protein 42 homolog / 0.742
5fl3 ADPPili retraction protein PilT / 0.742
2x2r ADPKinesin-like protein KIF11 / 0.741
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.741
1z0f GDPRas-related protein Rab-14 / 0.740
4hi0 GDPUrease accessory protein UreG / 0.740
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.739
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.739
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.738
4ldj GDPGTPase KRas / 0.738
4epx GDPGTPase KRas / 0.737
4lv6 GDPGTPase KRas / 0.737
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.736
4wa7 GDPGTPase KRas / 0.736
4zca ADPKinesin-like protein KIF11 / 0.736
4a1z ADPKinesin-like protein KIF11 / 0.734
4a51 ADPKinesin-like protein KIF11 / 0.734
5aun ADPIron-sulfur cluster carrier protein / 0.733
1w5t ADPORC1-type DNA replication protein 2 / 0.729
3tkl GTPRas-related protein Rab-1A / 0.729
2cea ADPATP-dependent zinc metalloprotease FtsH / 0.728
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.728
4a28 ADPKinesin-like protein KIF11 / 0.728
4ap0 ADPKinesin-like protein KIF11 / 0.728
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.727
1ii6 ADPKinesin-like protein KIF11 / 0.726
3cob ADPKinesin heavy chain-like protein / 0.726
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.726
3cf0 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.725
1ny5 ADPTranscriptional regulator (NtrC family) / 0.724
3bbp GTPRas-related protein Rab-6A / 0.724
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.724
3x1w GDPRas-related protein Rap-1b / 0.724
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.723
3kuc GDPRas-related protein Rap-1A / 0.723
3nbx ADPATPase RavA 3.6.3 0.720
1wdt GTPElongation factor G (EF-G-2) / 0.719
4kod ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.719
3kud GDPGTPase HRas / 0.718
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.718
1b7t ADPMyosin heavy chain, striated muscle / 0.717
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.717
3ea5 GDPGTP-binding nuclear protein Ran / 0.717
3m0e ATPTranscriptional regulator (NtrC family) / 0.717
4cf7 ADPAdenylate kinase / 0.717
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.716
2zro ADPProtein RecA / 0.716
2hld ANPATP synthase subunit alpha, mitochondrial / 0.715
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.715
4itr GDPCell division control protein 42 homolog / 0.715
4ww4 ADPRuvB-like helicase / 0.715
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.714
1fnn ADPORC1-type DNA replication protein / 0.714
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.713
4lpk GDPGTPase KRas / 0.713
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.712
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.711
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.710
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.710
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.710
1g16 GDPRas-related protein SEC4 / 0.709
4ys0 ADPProtein translocase subunit SecA / 0.708
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.706
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.706
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.705
4i1v ADPDephospho-CoA kinase / 0.705
4jky ADPAdenylate kinase / 0.705
2bku GTPGTP-binding nuclear protein Ran / 0.703
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.703
4yqf GDPSeptin-9 / 0.703
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.702
4hse ADPChaperone protein ClpB / 0.702
4idp GNPAtlastin-1 3.6.5 0.701
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.700
1z6t ADPApoptotic protease-activating factor 1 / 0.700
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.699
4dxa GSPRas-related protein Rap-1b / 0.699
1yra GDPGPN-loop GTPase PAB0955 / 0.698
3l1c ADPProtein claret segregational / 0.698
3tgp GNPGTPase HRas / 0.698
3r9i ADPSeptum site-determining protein MinD / 0.697
2ffq GSPRas-related protein Rab-6B / 0.696
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.696
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.696
2zr9 DTPProtein RecA / 0.696
2zs9 ADPPantothenate kinase 2.7.1.33 0.696
3t1t GDPProbable gliding protein mglA / 0.696
4hdq GNPRas-related protein Rap-1b / 0.696
4o2r GDPGTP-binding protein Rheb / 0.696
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.695
4g0n GNPGTPase HRas / 0.694
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.693
4k81 GTPGTPase HRas / 0.693
1z0a GDPRas-related protein Rab-2A / 0.692
1sq5 ADPPantothenate kinase 2.7.1.33 0.691
2c5l GTPGTPase HRas / 0.691
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.690
3mjh GTPRas-related protein Rab-5A / 0.690
2zs8 ADPPantothenate kinase 2.7.1.33 0.689
4g01 GDPRas-related protein RABF2b / 0.689
4y0v GDPADP-ribosylation factor 1, putative / 0.689
4ylg GDPADP-ribosylation factor 1, putative / 0.689
1a2b GSPTransforming protein RhoA / 0.688
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.688
2fe4 GDPRas-related protein Rab-6B / 0.688
3ref GDPRho family GTPase / 0.688
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.688
1sxj ADPReplication factor C subunit 5 / 0.687
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.687
1oix GDPRas-related protein Rab-11A / 0.686
3tlx ADPAdenylate kinase 2 / 0.686
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.685
5d3q GDPDynamin-1 3.6.5.5 0.685
3myk ANPMyosin-2 heavy chain / 0.684
5jlj GNPGTP-binding nuclear protein Ran / 0.684
3k3b ADPKinesin-like protein KIF11 / 0.683
4qos ADPPsp operon transcriptional activator / 0.683
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.682
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.681
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.681
2dpx GDPGTP-binding protein RAD / 0.680
3cph GDPRas-related protein SEC4 / 0.680
4goj GNPADP-ribosylation factor-like protein 3 / 0.680
4jl6 ADPAdenylate kinase / 0.680
4jlo ADPAdenylate kinase / 0.680
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.679
4dvg GSPRho family GTPase / 0.679
2gil GTPRas-related protein Rab-6A / 0.678
1m7b GTPRho-related GTP-binding protein RhoE / 0.677
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.677
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.677
1cxz GSPTransforming protein RhoA / 0.675
2xsz ATPRuvB-like 2 3.6.4.12 0.675
3bxz ADPProtein translocase subunit SecA / 0.675
4ike ADPAdenylate kinase / 0.675
4jl5 ADPAdenylate kinase / 0.675
4js0 GNPCell division control protein 42 homolog / 0.675
4jld ADPAdenylate kinase / 0.674
1w7i ADPUnconventional myosin-Va / 0.673
3law GNPRas-related protein Rab-7a / 0.673
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.673
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.672
3w3z GTPGTP-binding nuclear protein Ran / 0.672
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.672
1d5c GDPGTPase (Rab6) / 0.671
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.671
4oi2 ADPProtein clpf-1 / 0.670
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.670
4xvq GNPGTPase HRas / 0.670
1x1r GDPRas-related protein M-Ras / 0.669
2bc9 GNPGuanylate-binding protein 1 / 0.669
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.669
3uk6 ADPRuvB-like 2 3.6.4.12 0.669
4iok ADPFormate--tetrahydrofolate ligase / 0.669
4q03 GDPGTPase KRas / 0.669
4xvr GNPGTPase HRas / 0.669
2vor ACPFolylpolyglutamate synthase / 0.668
2zet GTPRas-related protein Rab-27B / 0.667
4l9s GDPGTPase HRas / 0.667
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.666
2gm1 ADPKinesin-like protein KIF11 / 0.666
2vos ADPFolylpolyglutamate synthase / 0.665
4q02 GDPGTPase KRas / 0.665
4qnr ATPPsp operon transcriptional activator / 0.665
5c3c ADPCbbQ/NirQ/NorQ domain protein / 0.665
1am4 GNPCell division control protein 42 homolog / 0.664
1z0d GDPRas-related protein Rab-5C / 0.664
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.664
3x1z GNPRas-related protein Rap-1b / 0.664
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.663
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.662
1zc4 GNPRas-related protein Ral-A / 0.662
2zyt PPSSulfotransferase 1 family member D1 / 0.662
4jjz ADPFormate--tetrahydrofolate ligase / 0.662
4ql3 GDPGTPase KRas / 0.662
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.661
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
1v8k ANPKinesin-like protein KIF2C / 0.661
2q3f GNPRas-related GTP-binding protein D / 0.660
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.659
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.659
4ovi N01Phenylacetone monooxygenase 1.14.13.92 0.659
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.659
2rgg GNPGTPase HRas / 0.658
2zsb ADPPantothenate kinase 2.7.1.33 0.658
3ddc GNPGTPase HRas / 0.658
3pit GNPRas-related protein M-Ras / 0.658
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.658
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.658
2ql6 ADPNicotinamide riboside kinase 1 / 0.657
1g17 GNPRas-related protein SEC4 / 0.655
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.655
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.655
2bme GNPRas-related protein Rab-4A / 0.655
3q5d GDPAtlastin-1 3.6.5 0.655
4idn GNPAtlastin-1 3.6.5 0.655
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.654
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.653
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.653
2vp4 DCPDeoxynucleoside kinase / 0.653
4kvg GTPRas-related protein Rap-1A / 0.653
2bbw GP5Adenylate kinase 4, mitochondrial / 0.652
3k9l GNPGTPase HRas / 0.652
3kko GNPRas-related protein M-Ras / 0.652
1wa5 GTPGTP-binding nuclear protein Ran / 0.650
2eck ADPAdenylate kinase / 0.650
2ewv ADPTwitching motility protein PilT / 0.650
3dm5 GDPSignal recognition particle 54 kDa protein / 0.650