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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
3kji ADP CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 1.073
5aun ADPIron-sulfur cluster carrier protein / 0.818
4rz3 ADPSite-determining protein / 0.817
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.802
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.791
4jlo ADPAdenylate kinase / 0.790
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.788
4cf7 ADPAdenylate kinase / 0.773
4jl6 ADPAdenylate kinase / 0.773
4ike ADPAdenylate kinase / 0.772
4z54 GDPNeuronal-specific septin-3 / 0.772
4jl5 ADPAdenylate kinase / 0.771
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.770
4jky ADPAdenylate kinase / 0.770
4jld ADPAdenylate kinase / 0.770
3ea0 ATPATPase, ParA family / 0.768
1z0a GDPRas-related protein Rab-2A / 0.767
3ieu GDPGTPase Era / 0.767
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.764
4lhv GDPRas-related protein Rab-8A / 0.763
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.763
4qbh AP5Adenylate kinase / 0.761
3t1t GDPProbable gliding protein mglA / 0.756
4epx GDPGTPase KRas / 0.754
1z2a GDPRas-related protein Rab-23 / 0.753
3tlx ADPAdenylate kinase 2 / 0.753
4o3m ADPBloom syndrome protein 3.6.4.12 0.751
3vhx GTPADP-ribosylation factor 6 / 0.750
3kud GDPGTPase HRas / 0.748
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.747
4wa7 GDPGTPase KRas / 0.746
4luc GDPGTPase KRas / 0.745
1jx2 ADPMyosin-2 heavy chain / 0.744
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.744
4gp6 ADPMetallophosphoesterase / 0.744
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.743
4ncl GDPEukaryotic translation initiation factor 5B / 0.743
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.742
3fkq ATPNtrC-like two-domain protein / 0.741
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.740
4lpk GDPGTPase KRas / 0.740
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.739
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.739
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.739
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.739
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.739
1yra GDPGPN-loop GTPase PAB0955 / 0.737
2fna ADPUncharacterized protein / 0.737
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.737
3ea5 GDPGTP-binding nuclear protein Ran / 0.737
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.736
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.735
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.735
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.735
3tqc ADPPantothenate kinase / 0.735
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.735
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.734
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.734
1oix GDPRas-related protein Rab-11A / 0.734
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.734
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.734
3mjh GTPRas-related protein Rab-5A / 0.733
1w5s ADPORC1-type DNA replication protein 2 / 0.732
1z0d GDPRas-related protein Rab-5C / 0.732
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.732
3kuc GDPRas-related protein Rap-1A / 0.730
3pcr GTPADP-ribosylation factor 6 / 0.730
3r9i ADPSeptum site-determining protein MinD / 0.730
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.730
4pjk ADPMyosin-2 heavy chain / 0.730
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.729
3hpq AP5Adenylate kinase / 0.729
3kb1 ADPIron-sulfur cluster carrier protein / 0.729
2eck ADPAdenylate kinase / 0.728
3b1x GNPFerrous iron transport protein B / 0.728
4pfp ADPUnconventional myosin-VI / 0.728
1b7t ADPMyosin heavy chain, striated muscle / 0.727
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.727
1wbb ADPDNA mismatch repair protein MutS / 0.727
3q9l ATPSeptum site-determining protein MinD / 0.727
1mma ADPMyosin-2 heavy chain / 0.726
4hi0 GDPUrease accessory protein UreG / 0.724
1z0f GDPRas-related protein Rab-14 / 0.723
4cdg ADPBloom syndrome protein 3.6.4.12 0.723
4o2l GTPGTP-binding protein Rheb / 0.723
4tq9 GDPGTPase KRas / 0.723
4ylg GDPADP-ribosylation factor 1, putative / 0.723
1mmg AGSMyosin-2 heavy chain / 0.722
1sq5 ADPPantothenate kinase 2.7.1.33 0.722
4goj GNPADP-ribosylation factor-like protein 3 / 0.722
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.721
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.721
2j5x GSPADP-ribosylation factor 6 / 0.721
2qen ADPWalker-Type ATPase / 0.721
4dso GSPGTPase KRas / 0.721
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.721
1d5c GDPGTPase (Rab6) / 0.720
4lrw GDPGTPase KRas / 0.720
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.720
2zts ADPUncharacterized protein / 0.719
3ref GDPRho family GTPase / 0.719
3tjz GNPADP-ribosylation factor 1 / 0.719
1uad GNPRas-related protein Ral-A / 0.718
2gm1 ADPKinesin-like protein KIF11 / 0.718
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.718
4asu ADPATP synthase subunit alpha, mitochondrial / 0.718
4iok ADPFormate--tetrahydrofolate ligase / 0.718
4o2r GDPGTP-binding protein Rheb / 0.718
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.717
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.717
3q5d GDPAtlastin-1 3.6.5 0.717
4xvq GNPGTPase HRas / 0.717
1ow3 GDPTransforming protein RhoA / 0.716
2ce2 GDPGTPase HRas / 0.716
3x1w GDPRas-related protein Rap-1b / 0.716
4a28 ADPKinesin-like protein KIF11 / 0.716
4dsu GDPGTPase KRas / 0.716
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.715
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.715
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.714
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.714
2zrj AGSProtein RecA / 0.714
3kkq GDPRas-related protein M-Ras / 0.714
5fl3 ADPPili retraction protein PilT / 0.714
2q3f GNPRas-related GTP-binding protein D / 0.713
4pjj ADPUnconventional myosin-VI / 0.713
5bn3 ADPV-type ATP synthase alpha chain / 0.713
5bn3 ADPNEQ263 / 0.713
5jlj GNPGTP-binding nuclear protein Ran / 0.713
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.712
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.712
4xvu ATPATPase GET3 / 0.712
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.711
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.711
1w5t ADPORC1-type DNA replication protein 2 / 0.711
4dzz ADPPlasmid partitioning protein ParF / 0.711
4l9s GDPGTPase HRas / 0.711
4obe GDPGTPase KRas / 0.711
4q03 GDPGTPase KRas / 0.711
1fnn ADPORC1-type DNA replication protein / 0.710
2fe4 GDPRas-related protein Rab-6B / 0.710
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.710
4hse ADPChaperone protein ClpB / 0.710
4y0v GDPADP-ribosylation factor 1, putative / 0.710
5c46 GSPRas-related protein Rab-11A / 0.710
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.709
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.709
1rrg GDPADP-ribosylation factor 1 / 0.708
1x1r GDPRas-related protein M-Ras / 0.708
2y65 ADPKinesin heavy chain / 0.708
4pk4 ADPUnconventional myosin-VI / 0.708
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.707
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.707
4kvg GTPRas-related protein Rap-1A / 0.707
5di3 GNPADP-ribosylation factor-like protein 3 / 0.707
5d3q GDPDynamin-1 3.6.5.5 0.706
2c98 ADPPsp operon transcriptional activator / 0.705
4oi2 ADPProtein clpf-1 / 0.705
5hpy GDPTransforming protein RhoA / 0.705
2x2r ADPKinesin-like protein KIF11 / 0.704
2zfi ADPKinesin-like protein KIF1A / 0.704
2l0x GDPGTP-binding protein Rheb / 0.703
2pg2 ADPKinesin-like protein KIF11 / 0.703
3k9l GNPGTPase HRas / 0.703
3oes GNPGTPase RhebL1 / 0.703
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.702
3l9h ADPKinesin-like protein KIF11 / 0.702
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.702
1l8q ADPChromosomal replication initiator protein DnaA / 0.701
1yu9 GNPRas-related protein Rab-4A / 0.701
4b7b ADPKinesin-like protein KIF11 / 0.701
3d8b ADPFidgetin-like protein 1 3.6.4 0.700
3kko GNPRas-related protein M-Ras / 0.700
4qos ADPPsp operon transcriptional activator / 0.700
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.699
2ql6 ADPNicotinamide riboside kinase 1 / 0.699
4lhw GNPRas-related protein Rab-8A / 0.699
4yqf GDPSeptin-9 / 0.699
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.698
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.698
4ys0 ADPProtein translocase subunit SecA / 0.698
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.698
1fmw ATPMyosin-2 heavy chain / 0.697
4l8g GDPGTPase KRas / 0.697
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.696
4a1z ADPKinesin-like protein KIF11 / 0.696
4dxa GSPRas-related protein Rap-1b / 0.696
1ank ANPAdenylate kinase / 0.695
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.695
1ny5 ADPTranscriptional regulator (NtrC family) / 0.695
5dha GNPGTP-binding nuclear protein Ran / 0.695
2rgc GNPGTPase HRas / 0.694
3cph GDPRas-related protein SEC4 / 0.694
3qbv GDPCell division control protein 42 homolog / 0.694
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.694
4ihq ADPConserved Archaeal protein / 0.694
3eg5 GNPCell division control protein 42 homolog / 0.693
3l1c ADPProtein claret segregational / 0.693
2g1q ADPKinesin-like protein KIF11 / 0.692
3a58 GNPGTP-binding protein RHO1 / 0.692
2zr9 DTPProtein RecA / 0.691
3tnf GNPRas-related protein Rab-8A / 0.691
3k1j ADPATP-dependent protease Lon / 0.690
1nly AGSCag alpha / 0.689
2fl2 ADPKinesin-like protein KIF11 / 0.689
4dls GNPGTPase HRas / 0.689
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.688
2uyi ADPKinesin-like protein KIF11 / 0.688
3thy ADPDNA mismatch repair protein Msh2 / 0.688
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.688
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.688
1zc3 GNPRas-related protein Ral-A / 0.687
1zc4 GNPRas-related protein Ral-A / 0.687
4epw GDPGTPase KRas / 0.687
4g0n GNPGTPase HRas / 0.687
4q02 GDPGTPase KRas / 0.687
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.687
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.686
2x7e ADPKinesin-like protein KIF11 / 0.686
2xsz ATPRuvB-like 2 3.6.4.12 0.686
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.686
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.686
5ftc ADPTPR domain protein / 0.686
2xae ADPKinesin-like protein KIF11 / 0.685
4ap0 ADPKinesin-like protein KIF11 / 0.685
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.684
3ddc GNPGTPase HRas / 0.684
3e5h GNPRas-related protein Rab-28 / 0.684
1e4v AP5Adenylate kinase / 0.683
3r9x GNPGTPase Era / 0.683
4a51 ADPKinesin-like protein KIF11 / 0.683
4zca ADPKinesin-like protein KIF11 / 0.683
1a2b GSPTransforming protein RhoA / 0.682
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.682
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.682
4mkh AP5Adenylate kinase / 0.682
4nh0 ATPESX secretion system protein EccC / 0.682
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.681
2c9o ADPRuvB-like 1 3.6.4.12 0.681
3dm5 GDPSignal recognition particle 54 kDa protein / 0.681
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.681
3qi2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.681
4b1v ATPActin, alpha skeletal muscle / 0.681
2gcp GSPRho-related GTP-binding protein RhoC / 0.680
1ibr GNPGTP-binding nuclear protein Ran / 0.679
4xoi GTPTransforming protein RhoA / 0.679
3myk ANPMyosin-2 heavy chain / 0.678
4ohx ADPProtein clpf-1 / 0.678
2xto GDPGTPase IMAP family member 2 / 0.677
3bxz ADPProtein translocase subunit SecA / 0.677
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.676
4dsn GCPGTPase KRas / 0.676
4qnr ATPPsp operon transcriptional activator / 0.676
1z2c GNPRho-related GTP-binding protein RhoC / 0.675
2rgb GNPGTPase HRas / 0.675
2rge GNPGTPase HRas / 0.675
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.675
3l8y GNPGTPase HRas / 0.675
3oiu GNPGTPase HRas / 0.675
3tgp GNPGTPase HRas / 0.675
3x1z GNPRas-related protein Rap-1b / 0.675
3c41 ANPAmino acid ABC transporter / 0.674
3i3s GNPGTPase HRas / 0.674
3lbh GNPGTPase HRas / 0.674
3oiv GNPGTPase HRas / 0.674
3pit GNPRas-related protein M-Ras / 0.674
4dlv GNPGTPase HRas / 0.674
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.674
5bn4 ANPV-type ATP synthase alpha chain / 0.674
1g16 GDPRas-related protein SEC4 / 0.673
2o8b ADPDNA mismatch repair protein Msh2 / 0.673
3zia ATPATP synthase subunit alpha, mitochondrial / 0.673
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.672
4d81 ADPAAA ATPase, central domain protein / 0.672
4hdq GNPRas-related protein Rap-1b / 0.672
2r9v ATPATP synthase subunit alpha / 0.671
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.671
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.671
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.670
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.669
2dft ADPShikimate kinase 2.7.1.71 0.667
4bub ADPUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase / 0.666
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.666
4xvr GNPGTPase HRas / 0.666
1dap NDPMeso-diaminopimelate D-dehydrogenase 1.4.1.16 0.665
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.665
3uk6 ADPRuvB-like 2 3.6.4.12 0.665
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.665
1xmv ADPProtein RecA / 0.664
4g01 GDPRas-related protein RABF2b / 0.663
4jjz ADPFormate--tetrahydrofolate ligase / 0.663
1am4 GNPCell division control protein 42 homolog / 0.662
2zro ADPProtein RecA / 0.662
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.662
1kmq GNPTransforming protein RhoA / 0.661
1qz5 ATPActin, alpha skeletal muscle / 0.661
1lfd GNPGTPase HRas / 0.660
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.659
2ad5 ADPCTP synthase / 0.658
2fg5 GNPRas-related protein Rab-31 / 0.658
2msc GDPMHC class I alpha chain / 0.657
4c30 ANPDNA helicase / 0.657
4ldj GDPGTPase KRas / 0.657
4nyj GNPGTPase HRas / 0.656
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.655
2rgg GNPGTPase HRas / 0.655
4dvg GSPRho family GTPase / 0.655
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.654
1z6t ADPApoptotic protease-activating factor 1 / 0.654
2iuu ADPDNA translocase FtsK / 0.654
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.654
3cob ADPKinesin heavy chain-like protein / 0.654
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.653
1w7i ADPUnconventional myosin-Va / 0.653
4ql3 GDPGTPase KRas / 0.653
4iei ADPGene 2 protein / 0.652
1atn ATPActin, alpha skeletal muscle / 0.651
1mwm ADPPlasmid segregation protein ParM / 0.651
2dpx GDPGTP-binding protein RAD / 0.651
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.651
3kz1 GSPTransforming protein RhoA / 0.651
1xtr GNPGTP-binding protein Rheb / 0.650
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.650