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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
2zr9 DTP Protein RecA

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2zr9 DTPProtein RecA / 1.006
2zrj AGSProtein RecA / 0.805
4ww4 ADPRuvB-like helicase / 0.790
2ql6 ADPNicotinamide riboside kinase 1 / 0.775
1zbd GTPRas-related protein Rab-3A / 0.768
5fl3 ADPPili retraction protein PilT / 0.767
2zro ADPProtein RecA / 0.762
2ffq GSPRas-related protein Rab-6B / 0.754
2gil GTPRas-related protein Rab-6A / 0.754
4ncl GDPEukaryotic translation initiation factor 5B / 0.753
2eck ADPAdenylate kinase / 0.752
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.749
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.749
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.748
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.746
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.745
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.744
3r9i ADPSeptum site-determining protein MinD / 0.743
1w5t ADPORC1-type DNA replication protein 2 / 0.741
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.740
1mmg AGSMyosin-2 heavy chain / 0.739
1x1r GDPRas-related protein M-Ras / 0.739
3q5d GDPAtlastin-1 3.6.5 0.738
4o2l GTPGTP-binding protein Rheb / 0.737
4mkh AP5Adenylate kinase / 0.735
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.734
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.734
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.734
2vor ACPFolylpolyglutamate synthase / 0.734
3w3z GTPGTP-binding nuclear protein Ran / 0.734
1gwn GTPRho-related GTP-binding protein RhoE / 0.733
1tu3 GNPRas-related protein Rab-5A / 0.732
2rgx AP5Adenylate kinase / 0.731
2bbw GP5Adenylate kinase 4, mitochondrial / 0.730
4iok ADPFormate--tetrahydrofolate ligase / 0.729
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.728
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.726
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.723
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.721
1z0d GDPRas-related protein Rab-5C / 0.721
2c9c ATPPsp operon transcriptional activator / 0.720
1m7b GTPRho-related GTP-binding protein RhoE / 0.719
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.718
3bbp GTPRas-related protein Rab-6A / 0.718
4zca ADPKinesin-like protein KIF11 / 0.718
1yra GDPGPN-loop GTPase PAB0955 / 0.717
1zio AP5Adenylate kinase / 0.717
1wdt GTPElongation factor G (EF-G-2) / 0.715
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.715
4qxa GTPRas-related protein Rab-9A / 0.715
2j5x GSPADP-ribosylation factor 6 / 0.713
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.713
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.712
2bku GTPGTP-binding nuclear protein Ran / 0.712
1ii6 ADPKinesin-like protein KIF11 / 0.711
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.711
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.709
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.708
3uk6 ADPRuvB-like 2 3.6.4.12 0.708
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.708
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.707
4xsg GSPTransforming protein RhoA / 0.707
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.706
3ieu GDPGTPase Era / 0.705
4epx GDPGTPase KRas / 0.704
4idp GNPAtlastin-1 3.6.5 0.703
2cl6 CAGGTPase HRas / 0.702
4hi0 GDPUrease accessory protein UreG / 0.701
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.700
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.700
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.697
5c46 GSPRas-related protein Rab-11A / 0.697
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.696
1w5s ADPORC1-type DNA replication protein 2 / 0.691
2bc9 GNPGuanylate-binding protein 1 / 0.691
3b1x GNPFerrous iron transport protein B / 0.691
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.691
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
2vf7 ADPUvrABC system protein A / 0.690
1xms ANPProtein RecA / 0.688
5dif GNPGTP-binding nuclear protein Ran / 0.688
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.687
3q9l ATPSeptum site-determining protein MinD / 0.687
1vg8 GNPRas-related protein Rab-7a / 0.686
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.686
4v02 ATPSite-determining protein / 0.686
4ys0 ADPProtein translocase subunit SecA / 0.686
5d3q GDPDynamin-1 3.6.5.5 0.686
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.685
1b7t ADPMyosin heavy chain, striated muscle / 0.685
4goj GNPADP-ribosylation factor-like protein 3 / 0.685
2qen ADPWalker-Type ATPase / 0.683
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.683
1g41 ADPATP-dependent protease ATPase subunit HslU / 0.682
3tgp GNPGTPase HRas / 0.682
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.682
4xvq GNPGTPase HRas / 0.682
2r9v ATPATP synthase subunit alpha / 0.681
5di3 GNPADP-ribosylation factor-like protein 3 / 0.681
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.679
2osb AP5Adenylate kinase / 0.679
1ibr GNPGTP-binding nuclear protein Ran / 0.678
2dft ADPShikimate kinase 2.7.1.71 0.678
4o3m ADPBloom syndrome protein 3.6.4.12 0.678
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
3aez GDPPantothenate kinase 2.7.1.33 0.674
3kuc GDPRas-related protein Rap-1A / 0.674
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.673
2qaj AP5Adenylate kinase / 0.673
3a6p GTPGTP-binding nuclear protein Ran / 0.672
2vos ADPFolylpolyglutamate synthase / 0.671
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.671
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.670
2rgg GNPGTPase HRas / 0.670
2vcz VC3Hematopoietic prostaglandin D synthase / 0.670
3ddc GNPGTPase HRas / 0.670
1yzq GNPRas-related protein Rab-6A / 0.669
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.669
2bme GNPRas-related protein Rab-4A / 0.669
3kko GNPRas-related protein M-Ras / 0.669
4oi2 ADPProtein clpf-1 / 0.669
3pit GNPRas-related protein M-Ras / 0.668
1esn ANPPantothenate kinase 2.7.1.33 0.667
1lfd GNPGTPase HRas / 0.667
2rgc GNPGTPase HRas / 0.667
3oiv GNPGTPase HRas / 0.667
4dlx GNPGTPase HRas / 0.667
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.666
1k5d GNPGTP-binding nuclear protein Ran / 0.665
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.665
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.665
3l1c ADPProtein claret segregational / 0.665
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.665
3tjz GNPADP-ribosylation factor 1 / 0.663
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.663
1sxj ADPReplication factor C subunit 5 / 0.661
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.660
1okk GCPSignal recognition particle protein / 0.659
1okk GCPSignal recognition particle receptor FtsY / 0.659
1xp8 AGSProtein RecA / 0.659
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.658
3kc1 2T6Fructose-1,6-bisphosphatase 1 3.1.3.11 0.658
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.657
4luc GDPGTPase KRas / 0.657
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.657
1a4r GNHCell division control protein 42 homolog / 0.656
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.656
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.656
1xmv ADPProtein RecA / 0.655
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.654
3x1z GNPRas-related protein Rap-1b / 0.654
4hdo GNPRas-related protein Rap-1b / 0.654
4fid GDPG protein alpha subunit, putative / 0.653
2iut AGSDNA translocase FtsK / 0.652
2yeg XQGHeat shock protein HSP 90-alpha / 0.652
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.652
4tq9 GDPGTPase KRas / 0.652
3af0 GDPPantothenate kinase 2.7.1.33 0.651
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.650
2zs9 ADPPantothenate kinase 2.7.1.33 0.650
3eg5 GNPCell division control protein 42 homolog / 0.650
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.650