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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
1w7i ADP Unconventional myosin-Va

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1w7i ADPUnconventional myosin-Va / 0.902
1jx2 ADPMyosin-2 heavy chain / 0.797
4pfp ADPUnconventional myosin-VI / 0.785
4pjj ADPUnconventional myosin-VI / 0.782
4pjk ADPMyosin-2 heavy chain / 0.764
1b7t ADPMyosin heavy chain, striated muscle / 0.763
4pk4 ADPUnconventional myosin-VI / 0.761
4db1 ANPMyosin-7 / 0.755
1fmw ATPMyosin-2 heavy chain / 0.752
1mma ADPMyosin-2 heavy chain / 0.727
1mmg AGSMyosin-2 heavy chain / 0.720
3myk ANPMyosin-2 heavy chain / 0.708
4a51 ADPKinesin-like protein KIF11 / 0.706
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.705
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.705
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.705
4jky ADPAdenylate kinase / 0.703
4jld ADPAdenylate kinase / 0.702
1z0a GDPRas-related protein Rab-2A / 0.700
2gm1 ADPKinesin-like protein KIF11 / 0.700
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.700
3tqc ADPPantothenate kinase / 0.699
4jl6 ADPAdenylate kinase / 0.699
1z6t ADPApoptotic protease-activating factor 1 / 0.698
2qen ADPWalker-Type ATPase / 0.697
3ref GDPRho family GTPase / 0.697
4jl5 ADPAdenylate kinase / 0.697
4jsy GTPMetallophosphoesterase / 0.696
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.695
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.694
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.693
3tlx ADPAdenylate kinase 2 / 0.693
4jlo ADPAdenylate kinase / 0.692
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.689
4dso GSPGTPase KRas / 0.689
4iei ADPGene 2 protein / 0.689
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.688
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.687
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.687
4qbh AP5Adenylate kinase / 0.685
1ny5 ADPTranscriptional regulator (NtrC family) / 0.684
4d81 ADPAAA ATPase, central domain protein / 0.684
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.683
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.683
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.682
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.682
4hi0 GDPUrease accessory protein UreG / 0.682
5aun ADPIron-sulfur cluster carrier protein / 0.682
5bn3 ADPV-type ATP synthase alpha chain / 0.682
5bn3 ADPNEQ263 / 0.682
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.681
4lrw GDPGTPase KRas / 0.681
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.680
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.680
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.680
4ike ADPAdenylate kinase / 0.680
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.678
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.678
1m7b GTPRho-related GTP-binding protein RhoE / 0.678
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.678
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.677
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.677
2y65 ADPKinesin heavy chain / 0.677
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.677
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.676
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
4qos ADPPsp operon transcriptional activator / 0.676
2x7e ADPKinesin-like protein KIF11 / 0.675
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.675
3tkl GTPRas-related protein Rab-1A / 0.675
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.674
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.674
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.674
2iuu ADPDNA translocase FtsK / 0.674
2pg2 ADPKinesin-like protein KIF11 / 0.674
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.673
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.673
2x2r ADPKinesin-like protein KIF11 / 0.673
2zts ADPUncharacterized protein / 0.673
4epx GDPGTPase KRas / 0.673
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
2zfi ADPKinesin-like protein KIF1A / 0.672
3k1j ADPATP-dependent protease Lon / 0.672
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.671
1z0d GDPRas-related protein Rab-5C / 0.671
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.671
4xvq GNPGTPase HRas / 0.671
1sdm ADPKinesin heavy chain-like protein / 0.670
3nbx ADPATPase RavA 3.6.3 0.670
4l8g GDPGTPase KRas / 0.670
1sq5 ADPPantothenate kinase 2.7.1.33 0.669
3cob ADPKinesin heavy chain-like protein / 0.669
3l9h ADPKinesin-like protein KIF11 / 0.669
3qbv GDPCell division control protein 42 homolog / 0.669
4epw GDPGTPase KRas / 0.669
4l9s GDPGTPase HRas / 0.669
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.669
4obe GDPGTPase KRas / 0.669
1oix GDPRas-related protein Rab-11A / 0.668
1w5s ADPORC1-type DNA replication protein 2 / 0.668
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.668
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
2rgx AP5Adenylate kinase / 0.668
4b7b ADPKinesin-like protein KIF11 / 0.668
1gwn GTPRho-related GTP-binding protein RhoE / 0.667
2gcp GSPRho-related GTP-binding protein RhoC / 0.667
4d0l GSPRas-related protein Rab-11A / 0.667
4luc GDPGTPase KRas / 0.667
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.666
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.666
4ldj GDPGTPase KRas / 0.666
1l2o ADPMyosin heavy chain, striated muscle / 0.665
1xts GTPGTP-binding protein Rheb / 0.665
2iut AGSDNA translocase FtsK / 0.664
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.664
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.664
3cph GDPRas-related protein SEC4 / 0.664
4dvg GSPRho family GTPase / 0.664
4gp6 ADPMetallophosphoesterase / 0.664
4lpk GDPGTPase KRas / 0.664
4xoi GTPTransforming protein RhoA / 0.664
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.663
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.663
4hse ADPChaperone protein ClpB / 0.663
4qm6 GTPMetallophosphoesterase / 0.663
1ank ANPAdenylate kinase / 0.662
1kqm ANPMyosin heavy chain, striated muscle / 0.662
2cl6 CAGGTPase HRas / 0.662
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.662
4cdg ADPBloom syndrome protein 3.6.4.12 0.662
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.661
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
2o8b ADPDNA mismatch repair protein Msh2 / 0.661
4ihq ADPConserved Archaeal protein / 0.661
4o2r GDPGTP-binding protein Rheb / 0.661
5bn4 ANPV-type ATP synthase alpha chain / 0.661
1g16 GDPRas-related protein SEC4 / 0.660
3zia ATPATP synthase subunit alpha, mitochondrial / 0.660
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
4itr GDPCell division control protein 42 homolog / 0.660
5fl3 ADPPili retraction protein PilT / 0.659
1svl ADPLarge T antigen 3.6.4 0.658
1uad GNPRas-related protein Ral-A / 0.658
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.658
4asu ADPATP synthase subunit alpha, mitochondrial / 0.658
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.658
3ea5 GDPGTP-binding nuclear protein Ran / 0.657
3oes GNPGTPase RhebL1 / 0.657
4oi2 ADPProtein clpf-1 / 0.657
4rz3 ADPSite-determining protein / 0.657
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.656
2eck ADPAdenylate kinase / 0.656
2uyi ADPKinesin-like protein KIF11 / 0.656
3kko GNPRas-related protein M-Ras / 0.656
3kz1 GSPTransforming protein RhoA / 0.656
3wyf GTPGTP-binding nuclear protein / 0.656
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.656
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.656
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.655
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.655
3m0e ATPTranscriptional regulator (NtrC family) / 0.655
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.655
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.655
1yu9 GNPRas-related protein Rab-4A / 0.654
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.653
2c9o ADPRuvB-like 1 3.6.4.12 0.653
2zrj AGSProtein RecA / 0.653
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.653
3kuc GDPRas-related protein Rap-1A / 0.653
5hpy GDPTransforming protein RhoA / 0.653
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.652
4ncl GDPEukaryotic translation initiation factor 5B / 0.652
4nu0 AP5Adenylate kinase / 0.652
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.652
1cxz GSPTransforming protein RhoA / 0.651
2oo7 AP5Adenylate kinase / 0.651
4y0v GDPADP-ribosylation factor 1, putative / 0.651
2eu8 AP5Adenylate kinase / 0.650
2hld ANPATP synthase subunit alpha, mitochondrial / 0.650
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
3thy ADPDNA mismatch repair protein Msh2 / 0.650
4xsg GSPTransforming protein RhoA / 0.650
5ftc ADPTPR domain protein / 0.650