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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
2dft ADP Shikimate kinase 2.7.1.71

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2dft ADPShikimate kinase 2.7.1.71 1.030
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.740
1e4y AP5Adenylate kinase / 0.734
1zbd GTPRas-related protein Rab-3A / 0.725
4jl5 ADPAdenylate kinase / 0.721
3l1c ADPProtein claret segregational / 0.714
2xsz ATPRuvB-like 2 3.6.4.12 0.713
4b7b ADPKinesin-like protein KIF11 / 0.712
3r9i ADPSeptum site-determining protein MinD / 0.709
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.707
1ibr GNPGTP-binding nuclear protein Ran / 0.706
4ww4 ADPRuvB-like helicase / 0.706
4jlo ADPAdenylate kinase / 0.705
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.705
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.704
1w5s ADPORC1-type DNA replication protein 2 / 0.702
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.702
4hse ADPChaperone protein ClpB / 0.693
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.691
2c96 ATPPsp operon transcriptional activator / 0.691
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.690
1p9w ANPType II secretion system protein E / 0.690
4jl6 ADPAdenylate kinase / 0.690
4qos ADPPsp operon transcriptional activator / 0.689
2eck ADPAdenylate kinase / 0.688
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.688
2ql6 ADPNicotinamide riboside kinase 1 / 0.686
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.684
1ny5 ADPTranscriptional regulator (NtrC family) / 0.683
3t1t GDPProbable gliding protein mglA / 0.682
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.680
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.680
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.680
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.680
4idn GNPAtlastin-1 3.6.5 0.680
4o25 GTPGTP-binding protein Rheb / 0.680
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.678
1mmg AGSMyosin-2 heavy chain / 0.678
2zr9 DTPProtein RecA / 0.678
1z0a GDPRas-related protein Rab-2A / 0.677
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.677
3tlx ADPAdenylate kinase 2 / 0.677
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.676
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.676
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.675
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.675
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.675
3myk ANPMyosin-2 heavy chain / 0.674
4mkf AP5Adenylate kinase / 0.674
1lfd GNPGTPase HRas / 0.673
5l3s GNPSignal recognition particle receptor FtsY / 0.673
1ank ANPAdenylate kinase / 0.672
1w5t ANPORC1-type DNA replication protein 2 / 0.672
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.672
5aun ADPIron-sulfur cluster carrier protein / 0.672
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.671
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
3ddc GNPGTPase HRas / 0.671
3rsl GNPGTPase HRas / 0.671
5k5z ANPUncharacterized protein / 0.671
1ii6 ADPKinesin-like protein KIF11 / 0.670
1z0d GDPRas-related protein Rab-5C / 0.670
2r9v ATPATP synthase subunit alpha / 0.670
2rgx AP5Adenylate kinase / 0.669
4o2r GDPGTP-binding protein Rheb / 0.669
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
4ike ADPAdenylate kinase / 0.668
4o2l GTPGTP-binding protein Rheb / 0.668
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.667
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.667
3pit GNPRas-related protein M-Ras / 0.667
4db1 ANPMyosin-7 / 0.667
4pk4 ADPUnconventional myosin-VI / 0.666
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.665
3k1j ADPATP-dependent protease Lon / 0.665
3mjh GTPRas-related protein Rab-5A / 0.665
3w3z GTPGTP-binding nuclear protein Ran / 0.665
4pjk ADPMyosin-2 heavy chain / 0.665
2fl2 ADPKinesin-like protein KIF11 / 0.664
2j5x GSPADP-ribosylation factor 6 / 0.664
2zrj AGSProtein RecA / 0.664
4gp6 ADPMetallophosphoesterase / 0.664
4zca ADPKinesin-like protein KIF11 / 0.664
1jx2 ADPMyosin-2 heavy chain / 0.663
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.663
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
3sop GDPNeuronal-specific septin-3 / 0.663
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.663
4pfp ADPUnconventional myosin-VI / 0.663
1fnn ADPORC1-type DNA replication protein / 0.662
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.662
3bc1 GNPRas-related protein Rab-27A / 0.661
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.660
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.660
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.660
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.660
2c9o ADPRuvB-like 1 3.6.4.12 0.659
2ffq GSPRas-related protein Rab-6B / 0.659
3b1x GNPFerrous iron transport protein B / 0.659
3d8b ADPFidgetin-like protein 1 3.6.4 0.659
4ys0 ADPProtein translocase subunit SecA / 0.659
1ake AP5Adenylate kinase / 0.658
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.658
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.658
1mma ADPMyosin-2 heavy chain / 0.657
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.657
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.657
1z2c GNPRho-related GTP-binding protein RhoC / 0.656
3kko GNPRas-related protein M-Ras / 0.656
3kuc GDPRas-related protein Rap-1A / 0.656
3vtk ADPThymidine kinase / 0.656
4e03 ADPPlasmid partitioning protein ParF / 0.656
1s1c GNPTransforming protein RhoA / 0.655
1sxj AGSReplication factor C subunit 1 / 0.655
2ikf UTPPoly(A) polymerase, putative / 0.655
3ftq GNPSeptin-2 / 0.655
3kc1 2T6Fructose-1,6-bisphosphatase 1 3.1.3.11 0.655
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.655
4dxa GSPRas-related protein Rap-1b / 0.655
4dzz ADPPlasmid partitioning protein ParF / 0.655
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.655
4xvq GNPGTPase HRas / 0.655
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.654
1m7b GTPRho-related GTP-binding protein RhoE / 0.654
2bbw GP5Adenylate kinase 4, mitochondrial / 0.654
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.654
2o8b ADPDNA mismatch repair protein Msh2 / 0.654
3k9l GNPGTPase HRas / 0.654
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.654
3tnf GNPRas-related protein Rab-8A / 0.654
4g0n GNPGTPase HRas / 0.654
4hi0 GDPUrease accessory protein UreG / 0.654
5di3 GNPADP-ribosylation factor-like protein 3 / 0.654
1k5d GNPGTP-binding nuclear protein Ran / 0.653
1kmq GNPTransforming protein RhoA / 0.653
1w5t ADPORC1-type DNA replication protein 2 / 0.653
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.653
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.653
3lbh GNPGTPase HRas / 0.653
3zia ATPATP synthase subunit alpha, mitochondrial / 0.653
1uad GNPRas-related protein Ral-A / 0.652
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.652
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.652
3kkq GDPRas-related protein M-Ras / 0.652
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.652
4lrw GDPGTPase KRas / 0.652
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.651
2bku GTPGTP-binding nuclear protein Ran / 0.651
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.651
2qen ADPWalker-Type ATPase / 0.651
3gfd FMNIodotyrosine deiodinase 1 1.21.1.1 0.651
3l9h ADPKinesin-like protein KIF11 / 0.651
3x1z GNPRas-related protein Rap-1b / 0.651
4dvg GSPRho family GTPase / 0.651
1dvr ATFAdenylate kinase / 0.650
1l8q ADPChromosomal replication initiator protein DnaA / 0.650
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.650
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.650
2msc GDPMHC class I alpha chain / 0.650
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.650
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.650
3cph GDPRas-related protein SEC4 / 0.650
4ap0 ADPKinesin-like protein KIF11 / 0.650
4hdo GNPRas-related protein Rap-1b / 0.650
4jky ADPAdenylate kinase / 0.650
4l8g GDPGTPase KRas / 0.650
4luc GDPGTPase KRas / 0.650
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.650
5dif GNPGTP-binding nuclear protein Ran / 0.650