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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
5da9 AGS Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5da9 AGSUncharacterized protein / 1.141
5dac AGSUncharacterized protein / 0.896
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.779
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.726
1sdm ADPKinesin heavy chain-like protein / 0.725
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.721
3cob ADPKinesin heavy chain-like protein / 0.720
4mkf AP5Adenylate kinase / 0.720
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.715
3w3z GTPGTP-binding nuclear protein Ran / 0.715
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.713
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.713
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.712
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.711
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.710
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.710
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.709
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.708
2hld ANPATP synthase subunit alpha, mitochondrial / 0.708
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.708
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.708
2j5x GSPADP-ribosylation factor 6 / 0.706
4qm6 GTPMetallophosphoesterase / 0.706
2gcp GSPRho-related GTP-binding protein RhoC / 0.705
1t91 GTPRas-related protein Rab-7a / 0.703
4dvg GSPRho family GTPase / 0.702
4gp6 ADPMetallophosphoesterase / 0.702
2xae ADPKinesin-like protein KIF11 / 0.700
5jlj GNPGTP-binding nuclear protein Ran / 0.700
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.699
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.698
5dha GNPGTP-binding nuclear protein Ran / 0.697
5ftc ADPTPR domain protein / 0.696
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.695
3q5d GDPAtlastin-1 3.6.5 0.694
3ftq GNPSeptin-2 / 0.693
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.693
3c41 ANPAmino acid ABC transporter / 0.692
4qnr ATPPsp operon transcriptional activator / 0.692
1m7b GTPRho-related GTP-binding protein RhoE / 0.689
1wdt GTPElongation factor G (EF-G-2) / 0.689
4d0l GSPRas-related protein Rab-11A / 0.689
5c46 GSPRas-related protein Rab-11A / 0.689
4l8g GDPGTPase KRas / 0.688
3l9h ADPKinesin-like protein KIF11 / 0.687
4qxa GTPRas-related protein Rab-9A / 0.687
2r9v ATPATP synthase subunit alpha / 0.686
2uyi ADPKinesin-like protein KIF11 / 0.686
4b7b ADPKinesin-like protein KIF11 / 0.685
4obe GDPGTPase KRas / 0.685
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.685
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.684
4q03 GDPGTPase KRas / 0.684
4ql3 GDPGTPase KRas / 0.684
2c5l GTPGTPase HRas / 0.683
3hqd ANPKinesin-like protein KIF11 / 0.683
1kqm ANPMyosin heavy chain, striated muscle / 0.682
2q2z ADPKinesin-like protein KIF11 / 0.680
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.680
3law GNPRas-related protein Rab-7a / 0.679
4a51 ADPKinesin-like protein KIF11 / 0.679
2c9c ATPPsp operon transcriptional activator / 0.678
3tgp GNPGTPase HRas / 0.676
4luc GDPGTPase KRas / 0.676
1ky2 GNPGTP-binding protein YPT7 / 0.675
3tjz GNPADP-ribosylation factor 1 / 0.674
4idp GNPAtlastin-1 3.6.5 0.674
1xtr GNPGTP-binding protein Rheb / 0.673
2zfi ADPKinesin-like protein KIF1A / 0.673
2o8b ADPDNA mismatch repair protein Msh2 / 0.672
2x7e ADPKinesin-like protein KIF11 / 0.672
4mkh AP5Adenylate kinase / 0.672
1bxr ANPCarbamoyl-phosphate synthase large chain / 0.671
2osb AP5Adenylate kinase / 0.671
3kz1 GSPTransforming protein RhoA / 0.671
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.669
4q02 GDPGTPase KRas / 0.669
4qos ADPPsp operon transcriptional activator / 0.669
1yrs ADPKinesin-like protein KIF11 / 0.668
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.668
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.667
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.667
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.666
2x2r ADPKinesin-like protein KIF11 / 0.666
4o3m ADPBloom syndrome protein 3.6.4.12 0.666
4pk4 ADPUnconventional myosin-VI / 0.666
1cxz GSPTransforming protein RhoA / 0.665
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.665
1svw GTPProbable GTP-binding protein EngB / 0.665
2gm1 ADPKinesin-like protein KIF11 / 0.665
4dso GSPGTPase KRas / 0.664
4pjj ADPUnconventional myosin-VI / 0.664
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.663
2qen ADPWalker-Type ATPase / 0.663
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.663
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.663
3qbt GNPRas-related protein Rab-8A / 0.663
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.662
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
1lfd GNPGTPase HRas / 0.662
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.662
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.662
4k81 GTPGTPase HRas / 0.662
5fl3 ADPPili retraction protein PilT / 0.662
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.661
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
3wyf GTPGTP-binding nuclear protein / 0.661
4kvg GTPRas-related protein Rap-1A / 0.661
1wbb ADPDNA mismatch repair protein MutS / 0.660
2jlr ANPGenome polyprotein 3.4.21.91 0.660
3x1z GNPRas-related protein Rap-1b / 0.660
4idn GNPAtlastin-1 3.6.5 0.660
5di3 GNPADP-ribosylation factor-like protein 3 / 0.660
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.659
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.659
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.659
4uj5 GNPRas-related protein Rab-11A / 0.659
1fmw ATPMyosin-2 heavy chain / 0.658
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.658
4mit GTPRho-related protein racC / 0.658
5ftf ADPTPR domain protein / 0.658
2c96 ATPPsp operon transcriptional activator / 0.657
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.657
4yqf GDPSeptin-9 / 0.657
4zca ADPKinesin-like protein KIF11 / 0.657
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.656
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.656
2cls GTPRho-related GTP-binding protein Rho6 / 0.656
5cyo GDPSeptin-9 / 0.656
5cyp GSPSeptin-9 / 0.656
2iut AGSDNA translocase FtsK / 0.655
1a2b GSPTransforming protein RhoA / 0.654
2gil GTPRas-related protein Rab-6A / 0.654
1f5n GNPGuanylate-binding protein 1 / 0.653
1w5s ADPORC1-type DNA replication protein 2 / 0.653
2rgg GNPGTPase HRas / 0.653
4asu ADPATP synthase subunit alpha, mitochondrial / 0.653
4qbg AP5Adenylate kinase / 0.653
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.652
4lhv GDPRas-related protein Rab-8A / 0.652
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.652
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.651
2pg2 ADPKinesin-like protein KIF11 / 0.650
3bxz ADPProtein translocase subunit SecA / 0.650
3tkl GTPRas-related protein Rab-1A / 0.650
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.650
4ol0 GTPGTP-binding nuclear protein Ran / 0.650