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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
3thy ADP DNA mismatch repair protein Msh2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3thy ADPDNA mismatch repair protein Msh2 / 0.999
4asu ADPATP synthase subunit alpha, mitochondrial / 0.767
2o8b ADPDNA mismatch repair protein Msh2 / 0.759
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.757
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.757
1wbb ADPDNA mismatch repair protein MutS / 0.748
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.745
4z54 GDPNeuronal-specific septin-3 / 0.743
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.742
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.742
1sxj ADPReplication factor C subunit 5 / 0.742
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.738
3tqc ADPPantothenate kinase / 0.738
1z6t ADPApoptotic protease-activating factor 1 / 0.737
4zca ADPKinesin-like protein KIF11 / 0.737
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.736
2fl2 ADPKinesin-like protein KIF11 / 0.735
4yqf GDPSeptin-9 / 0.734
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.733
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.733
2ffq GSPRas-related protein Rab-6B / 0.733
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.732
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.730
1z0a GDPRas-related protein Rab-2A / 0.729
2ql6 ADPNicotinamide riboside kinase 1 / 0.729
2pg2 ADPKinesin-like protein KIF11 / 0.728
2uyi ADPKinesin-like protein KIF11 / 0.728
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.725
3r9i ADPSeptum site-determining protein MinD / 0.725
4pjj ADPUnconventional myosin-VI / 0.725
1yrs ADPKinesin-like protein KIF11 / 0.724
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.721
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.721
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.721
4a51 ADPKinesin-like protein KIF11 / 0.721
1nly AGSCag alpha / 0.720
2fna ADPUncharacterized protein / 0.720
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.719
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.719
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.718
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.718
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.718
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.718
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.718
4cf7 ADPAdenylate kinase / 0.718
4ike ADPAdenylate kinase / 0.718
4o2l GTPGTP-binding protein Rheb / 0.718
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.717
2eck ADPAdenylate kinase / 0.717
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.717
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.716
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.716
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.715
4ihq ADPConserved Archaeal protein / 0.715
4qxa GTPRas-related protein Rab-9A / 0.715
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.715
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.714
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.713
2x2r ADPKinesin-like protein KIF11 / 0.713
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.713
2qen ADPWalker-Type ATPase / 0.712
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.711
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.711
2x7e ADPKinesin-like protein KIF11 / 0.711
3zia ATPATP synthase subunit alpha, mitochondrial / 0.711
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.710
3q5d GDPAtlastin-1 3.6.5 0.710
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.710
4gp6 ADPMetallophosphoesterase / 0.710
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.709
1oix GDPRas-related protein Rab-11A / 0.708
4ncl GDPEukaryotic translation initiation factor 5B / 0.708
5fl3 ADPPili retraction protein PilT / 0.708
1ake AP5Adenylate kinase / 0.707
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.707
2xae ADPKinesin-like protein KIF11 / 0.707
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.707
3pcr GTPADP-ribosylation factor 6 / 0.707
5cyo GDPSeptin-9 / 0.707
4iok ADPFormate--tetrahydrofolate ligase / 0.706
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.705
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.705
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.705
4jl5 ADPAdenylate kinase / 0.705
4jl6 ADPAdenylate kinase / 0.705
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.704
4dsu GDPGTPase KRas / 0.704
4o2r GDPGTP-binding protein Rheb / 0.704
4jld ADPAdenylate kinase / 0.703
4jlo ADPAdenylate kinase / 0.703
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.702
4dzz ADPPlasmid partitioning protein ParF / 0.702
4jsy GTPMetallophosphoesterase / 0.702
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.702
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.702
1jx2 ADPMyosin-2 heavy chain / 0.701
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.701
1xmv ADPProtein RecA / 0.701
3c41 ANPAmino acid ABC transporter / 0.701
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.700
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.700
2zet GTPRas-related protein Rab-27B / 0.700
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.699
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.699
3tlx ADPAdenylate kinase 2 / 0.699
4iei ADPGene 2 protein / 0.699
5bn3 ADPV-type ATP synthase alpha chain / 0.699
5bn3 ADPNEQ263 / 0.699
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.698
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.697
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.697
1xms ANPProtein RecA / 0.696
4a28 ADPKinesin-like protein KIF11 / 0.696
4hi0 GDPUrease accessory protein UreG / 0.696
4b7b ADPKinesin-like protein KIF11 / 0.695
4g01 GDPRas-related protein RABF2b / 0.695
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.694
1ny5 ADPTranscriptional regulator (NtrC family) / 0.694
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.694
2rgx AP5Adenylate kinase / 0.694
1a2b GSPTransforming protein RhoA / 0.693
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.693
4dso GSPGTPase KRas / 0.693
1zbd GTPRas-related protein Rab-3A / 0.692
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.692
3l9h ADPKinesin-like protein KIF11 / 0.692
4qos ADPPsp operon transcriptional activator / 0.692
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.691
1z2a GDPRas-related protein Rab-23 / 0.691
2ncd ADPProtein claret segregational / 0.691
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.691
2y65 ADPKinesin heavy chain / 0.691
5k5z ANPUncharacterized protein / 0.691
2fe4 GDPRas-related protein Rab-6B / 0.690
1rrg GDPADP-ribosylation factor 1 / 0.689
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.689
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.689
4y0v GDPADP-ribosylation factor 1, putative / 0.689
4ylg GDPADP-ribosylation factor 1, putative / 0.689
1z0d GDPRas-related protein Rab-5C / 0.688
2gm1 ADPKinesin-like protein KIF11 / 0.688
2hld ANPATP synthase subunit alpha, mitochondrial / 0.688
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
2zfi ADPKinesin-like protein KIF1A / 0.688
2zts ADPUncharacterized protein / 0.688
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.688
4qm6 GTPMetallophosphoesterase / 0.688
4wa7 GDPGTPase KRas / 0.688
2iut AGSDNA translocase FtsK / 0.687
3kkq GDPRas-related protein M-Ras / 0.687
4l8g GDPGTPase KRas / 0.687
4qnr ATPPsp operon transcriptional activator / 0.687
1d5c GDPGTPase (Rab6) / 0.686
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.686
1sq5 ADPPantothenate kinase 2.7.1.33 0.685
1x1r GDPRas-related protein M-Ras / 0.685
4lv6 GDPGTPase KRas / 0.685
4obe GDPGTPase KRas / 0.685
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.684
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
2q2z ADPKinesin-like protein KIF11 / 0.684
2r9v ATPATP synthase subunit alpha / 0.684
3b1x GNPFerrous iron transport protein B / 0.684
4epw GDPGTPase KRas / 0.684
4l9s GDPGTPase HRas / 0.684
5di3 GNPADP-ribosylation factor-like protein 3 / 0.684
1uad GNPRas-related protein Ral-A / 0.683
3qbv GDPCell division control protein 42 homolog / 0.683
4ldj GDPGTPase KRas / 0.683
4q02 GDPGTPase KRas / 0.683
4q03 GDPGTPase KRas / 0.683
4ql3 GDPGTPase KRas / 0.683
4tq9 GDPGTPase KRas / 0.683
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.682
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
3cob ADPKinesin heavy chain-like protein / 0.682
3x1w GDPRas-related protein Rap-1b / 0.682
4epx GDPGTPase KRas / 0.682
4pfp ADPUnconventional myosin-VI / 0.682
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.681
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
1yra GDPGPN-loop GTPase PAB0955 / 0.681
2ce2 GDPGTPase HRas / 0.681
2vor ACPFolylpolyglutamate synthase / 0.681
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.681
3k1j ADPATP-dependent protease Lon / 0.681
3kuc GDPRas-related protein Rap-1A / 0.681
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.681
1e4y AP5Adenylate kinase / 0.680
1g16 GDPRas-related protein SEC4 / 0.680
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.680
1sdm ADPKinesin heavy chain-like protein / 0.680
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.680
4e03 ADPPlasmid partitioning protein ParF / 0.680
5aun ADPIron-sulfur cluster carrier protein / 0.680
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.679
3kz1 GSPTransforming protein RhoA / 0.679
5ftc ADPTPR domain protein / 0.679
2xsz ATPRuvB-like 2 3.6.4.12 0.678
1w5t ADPORC1-type DNA replication protein 2 / 0.677
1l8q ADPChromosomal replication initiator protein DnaA / 0.676
3l1c ADPProtein claret segregational / 0.676
4o3m ADPBloom syndrome protein 3.6.4.12 0.676
4pk4 ADPUnconventional myosin-VI / 0.676
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.675
4lrw GDPGTPase KRas / 0.675
4rz3 ADPSite-determining protein / 0.675
4v02 ATPSite-determining protein / 0.675
4luc GDPGTPase KRas / 0.674
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.672
3k3b ADPKinesin-like protein KIF11 / 0.672
3qbt GNPRas-related protein Rab-8A / 0.672
5c46 GSPRas-related protein Rab-11A / 0.672
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.671
3tkl GTPRas-related protein Rab-1A / 0.671
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.670
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.670
2l0x GDPGTP-binding protein Rheb / 0.670
3kud GDPGTPase HRas / 0.670
4dxa GSPRas-related protein Rap-1b / 0.670
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.670
4xsg GSPTransforming protein RhoA / 0.670
2dpx GDPGTP-binding protein RAD / 0.669
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.669
4nh0 ATPESX secretion system protein EccC / 0.669
4pjk ADPMyosin-2 heavy chain / 0.669
1gwn GTPRho-related GTP-binding protein RhoE / 0.667
1m7b GTPRho-related GTP-binding protein RhoE / 0.667
1w5s ADPORC1-type DNA replication protein 2 / 0.667
4o25 GTPGTP-binding protein Rheb / 0.667
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.666
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.666
4d0l GSPRas-related protein Rab-11A / 0.666
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.665
2dr3 ADPUPF0273 protein PH0284 / 0.665
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
4hdq GNPRas-related protein Rap-1b / 0.665
4mkh AP5Adenylate kinase / 0.665
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.664
2rgg GNPGTPase HRas / 0.664
3ftq GNPSeptin-2 / 0.664
3kko GNPRas-related protein M-Ras / 0.664
3x1z GNPRas-related protein Rap-1b / 0.664
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.663
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.663
2bku GTPGTP-binding nuclear protein Ran / 0.663
2g1q ADPKinesin-like protein KIF11 / 0.663
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.663
2rge GNPGTPase HRas / 0.663
3pit GNPRas-related protein M-Ras / 0.663
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.663
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.663
5d3q GDPDynamin-1 3.6.5.5 0.662
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.661
3a6p GTPGTP-binding nuclear protein Ran / 0.661
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.661
4jky ADPAdenylate kinase / 0.661
2gil GTPRas-related protein Rab-6A / 0.660
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.660
3oee ANPATP synthase subunit alpha, mitochondrial / 0.660
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
4ffl ADPUncharacterized protein / 0.660
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.660
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.660
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.660
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.659
1zio AP5Adenylate kinase / 0.659
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.659
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.659
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.658
1rj9 GCPSignal recognition particle receptor FtsY / 0.657
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.657
1xtr GNPGTP-binding protein Rheb / 0.656
2c9c ATPPsp operon transcriptional activator / 0.656
3kc1 2T6Fructose-1,6-bisphosphatase 1 3.1.3.11 0.656
3t1t GDPProbable gliding protein mglA / 0.656
3vhx GTPADP-ribosylation factor 6 / 0.656
4cym GCPRas-related protein Rab-32 / 0.656
4db1 ANPMyosin-7 / 0.656
1cxz GSPTransforming protein RhoA / 0.654
2zro ADPProtein RecA / 0.654
1am4 GNPCell division control protein 42 homolog / 0.653
2q3f GNPRas-related GTP-binding protein D / 0.653
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.652
4goj GNPADP-ribosylation factor-like protein 3 / 0.652
4idn GNPAtlastin-1 3.6.5 0.652
4fid GDPG protein alpha subunit, putative / 0.651
1ow3 GDPTransforming protein RhoA / 0.650
1p9w ANPType II secretion system protein E / 0.650
1w7i ADPUnconventional myosin-Va / 0.650
3af0 GDPPantothenate kinase 2.7.1.33 0.650
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.650
4idp GNPAtlastin-1 3.6.5 0.650