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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
4ys0 ADP Protein translocase subunit SecA

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ys0 ADPProtein translocase subunit SecA / 1.084
5bn3 ADPV-type ATP synthase alpha chain / 0.810
5bn3 ADPNEQ263 / 0.810
4o3m ADPBloom syndrome protein 3.6.4.12 0.802
4ql3 GDPGTPase KRas / 0.801
3kuc GDPRas-related protein Rap-1A / 0.799
4epx GDPGTPase KRas / 0.794
1z2a GDPRas-related protein Rab-23 / 0.791
4g0n GNPGTPase HRas / 0.790
4z54 GDPNeuronal-specific septin-3 / 0.787
4q03 GDPGTPase KRas / 0.785
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.781
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.781
4wa7 GDPGTPase KRas / 0.781
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.780
1z0d GDPRas-related protein Rab-5C / 0.779
1d5c GDPGTPase (Rab6) / 0.778
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.778
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.778
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.776
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.774
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.772
2dpx GDPGTP-binding protein RAD / 0.771
4l8g GDPGTPase KRas / 0.771
4l9s GDPGTPase HRas / 0.768
4ldj GDPGTPase KRas / 0.768
4qxa GTPRas-related protein Rab-9A / 0.768
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.767
3kkq GDPRas-related protein M-Ras / 0.767
1ow3 GDPTransforming protein RhoA / 0.766
3x1z GNPRas-related protein Rap-1b / 0.766
4lv6 GDPGTPase KRas / 0.766
3mjh GTPRas-related protein Rab-5A / 0.765
4dlz GNPGTPase HRas / 0.765
4gp6 ADPMetallophosphoesterase / 0.763
4tq9 GDPGTPase KRas / 0.763
1jx2 ADPMyosin-2 heavy chain / 0.762
3i3s GNPGTPase HRas / 0.761
3k8y GNPGTPase HRas / 0.761
4epw GDPGTPase KRas / 0.761
4pfp ADPUnconventional myosin-VI / 0.761
1oix GDPRas-related protein Rab-11A / 0.760
4q02 GDPGTPase KRas / 0.760
1wbb ADPDNA mismatch repair protein MutS / 0.759
3cob ADPKinesin heavy chain-like protein / 0.758
4dsu GDPGTPase KRas / 0.758
1mmg AGSMyosin-2 heavy chain / 0.756
3r9i ADPSeptum site-determining protein MinD / 0.756
3q5d GDPAtlastin-1 3.6.5 0.755
4dxa GSPRas-related protein Rap-1b / 0.754
1sdm ADPKinesin heavy chain-like protein / 0.751
3x1w GDPRas-related protein Rap-1b / 0.751
1z0f GDPRas-related protein Rab-14 / 0.750
2pg2 ADPKinesin-like protein KIF11 / 0.750
5b2z GNPGTPase HRas / 0.750
2gil GTPRas-related protein Rab-6A / 0.749
2uyi ADPKinesin-like protein KIF11 / 0.749
2x2r ADPKinesin-like protein KIF11 / 0.749
3ddc GNPGTPase HRas / 0.749
4dls GNPGTPase HRas / 0.749
2gm1 ADPKinesin-like protein KIF11 / 0.748
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.748
4kvg GTPRas-related protein Rap-1A / 0.748
2j5x GSPADP-ribosylation factor 6 / 0.747
4a28 ADPKinesin-like protein KIF11 / 0.747
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.747
2ffq GSPRas-related protein Rab-6B / 0.746
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.746
1x1r GDPRas-related protein M-Ras / 0.745
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.745
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.745
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.745
2ce2 GDPGTPase HRas / 0.744
2o8b ADPDNA mismatch repair protein Msh2 / 0.744
3ea0 ATPATPase, ParA family / 0.744
4pjj ADPUnconventional myosin-VI / 0.744
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.743
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.743
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.743
3bxz ADPProtein translocase subunit SecA / 0.743
4cf7 ADPAdenylate kinase / 0.743
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.741
1b7t ADPMyosin heavy chain, striated muscle / 0.740
1tu3 GNPRas-related protein Rab-5A / 0.740
1l8q ADPChromosomal replication initiator protein DnaA / 0.738
2fe4 GDPRas-related protein Rab-6B / 0.738
2xae ADPKinesin-like protein KIF11 / 0.738
3ea5 GDPGTP-binding nuclear protein Ran / 0.738
2zfi ADPKinesin-like protein KIF1A / 0.737
3oiv GNPGTPase HRas / 0.736
3ref GDPRho family GTPase / 0.736
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.734
4luc GDPGTPase KRas / 0.734
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.734
4o2r GDPGTP-binding protein Rheb / 0.734
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.733
3lbi GNPGTPase HRas / 0.733
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.733
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.732
3a58 GNPGTP-binding protein RHO1 / 0.732
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.731
2rge GNPGTPase HRas / 0.731
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.731
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.731
4lpk GDPGTPase KRas / 0.731
4pjk ADPMyosin-2 heavy chain / 0.731
1ii6 ADPKinesin-like protein KIF11 / 0.730
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.730
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.730
1yzq GNPRas-related protein Rab-6A / 0.730
2cl6 CAGGTPase HRas / 0.730
2qen ADPWalker-Type ATPase / 0.730
4cdg ADPBloom syndrome protein 3.6.4.12 0.730
1n6l GTPRas-related protein Rab-5A / 0.729
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.729
2x7e ADPKinesin-like protein KIF11 / 0.728
4v02 ATPSite-determining protein / 0.728
4xvr GNPGTPase HRas / 0.728
1g17 GNPRas-related protein SEC4 / 0.727
1zbd GTPRas-related protein Rab-3A / 0.727
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.727
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.727
2rgc GNPGTPase HRas / 0.726
3lbn GNPGTPase HRas / 0.726
4k81 GTPGTPase HRas / 0.726
5c46 GSPRas-related protein Rab-11A / 0.726
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.725
4lhw GNPRas-related protein Rab-8A / 0.725
1mma ADPMyosin-2 heavy chain / 0.724
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.724
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.724
1z0a GDPRas-related protein Rab-2A / 0.723
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.723
4ncl GDPEukaryotic translation initiation factor 5B / 0.723
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.721
2bme GNPRas-related protein Rab-4A / 0.720
4itr GDPCell division control protein 42 homolog / 0.719
1vg8 GNPRas-related protein Rab-7a / 0.718
3wyf GTPGTP-binding nuclear protein / 0.718
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.717
3tso GNPRas-related protein Rab-25 / 0.717
4dlw GNPGTPase HRas / 0.717
4lrw GDPGTPase KRas / 0.717
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.716
4d0l GSPRas-related protein Rab-11A / 0.716
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.715
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.715
3k9l GNPGTPase HRas / 0.715
4dzz ADPPlasmid partitioning protein ParF / 0.715
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.714
1yu9 GNPRas-related protein Rab-4A / 0.714
3e5h GNPRas-related protein Rab-28 / 0.714
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.714
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.713
1ibr GNPGTP-binding nuclear protein Ran / 0.713
1xtr GNPGTP-binding protein Rheb / 0.713
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.713
2zts ADPUncharacterized protein / 0.712
4dsn GCPGTPase KRas / 0.712
4idn GNPAtlastin-1 3.6.5 0.712
4ihq ADPConserved Archaeal protein / 0.712
3l1c ADPProtein claret segregational / 0.710
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.709
1sxj AGSReplication factor C subunit 1 / 0.709
3l8y GNPGTPase HRas / 0.709
4jsy GTPMetallophosphoesterase / 0.709
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.708
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
1k5d GNPGTP-binding nuclear protein Ran / 0.708
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.708
4yqf GDPSeptin-9 / 0.708
1e4v AP5Adenylate kinase / 0.707
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.707
3bbp GTPRas-related protein Rab-6A / 0.707
3kud GDPGTPase HRas / 0.707
4cym GCPRas-related protein Rab-32 / 0.707
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.706
3tgp GNPGTPase HRas / 0.706
4a1z ADPKinesin-like protein KIF11 / 0.706
4ap0 ADPKinesin-like protein KIF11 / 0.706
2c9o ADPRuvB-like 1 3.6.4.12 0.705
3cph GDPRas-related protein SEC4 / 0.705
4zca ADPKinesin-like protein KIF11 / 0.704
5l3s GNPSignal recognition particle receptor FtsY / 0.704
1z2c GNPRho-related GTP-binding protein RhoC / 0.703
3vhx GTPADP-ribosylation factor 6 / 0.703
5aun ADPIron-sulfur cluster carrier protein / 0.703
3oes GNPGTPase RhebL1 / 0.702
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.702
1wdt GTPElongation factor G (EF-G-2) / 0.701
3zfd ANPChromosome-associated kinesin KIF4 / 0.701
4asu ADPATP synthase subunit alpha, mitochondrial / 0.701
1fnn ADPORC1-type DNA replication protein / 0.700
4db1 ANPMyosin-7 / 0.700
4mit GTPRho-related protein racC / 0.700
4o2l GTPGTP-binding protein Rheb / 0.700
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.698
2r9v ATPATP synthase subunit alpha / 0.698
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.698
3m0e ATPTranscriptional regulator (NtrC family) / 0.698
4lhv GDPRas-related protein Rab-8A / 0.698
4qm6 GTPMetallophosphoesterase / 0.698
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.697
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.697
1yrs ADPKinesin-like protein KIF11 / 0.697
3bc1 GNPRas-related protein Rab-27A / 0.697
1nly AGSCag alpha / 0.695
2fg5 GNPRas-related protein Rab-31 / 0.695
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.695
1m7b GTPRho-related GTP-binding protein RhoE / 0.694
1sq5 ADPPantothenate kinase 2.7.1.33 0.694
3rsl GNPGTPase HRas / 0.694
4idp GNPAtlastin-1 3.6.5 0.694
1f5n GNPGuanylate-binding protein 1 / 0.693
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.693
1oyy AGSATP-dependent DNA helicase RecQ 3.6.4.12 0.693
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.693
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.693
2c96 ATPPsp operon transcriptional activator / 0.692
3law GNPRas-related protein Rab-7a / 0.692
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.692
1rrg GDPADP-ribosylation factor 1 / 0.691
2rgg GNPGTPase HRas / 0.691
4g01 GDPRas-related protein RABF2b / 0.691
4hdq GNPRas-related protein Rap-1b / 0.691
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.690
2rgb GNPGTPase HRas / 0.690
3oiu GNPGTPase HRas / 0.690
3rs0 GNPGTPase HRas / 0.690
3rs4 GNPGTPase HRas / 0.690
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.690
4pk4 ADPUnconventional myosin-VI / 0.690
4xvq GNPGTPase HRas / 0.690
5ftc ADPTPR domain protein / 0.690
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.689
4dlt GNPGTPase HRas / 0.689
4dlv GNPGTPase HRas / 0.689
4hdo GNPRas-related protein Rap-1b / 0.689
4l9w GNPGTPase HRas / 0.689
3oiw GNPGTPase HRas / 0.688
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.688
4dlx GNPGTPase HRas / 0.688
1uad GNPRas-related protein Ral-A / 0.686
2zr9 DTPProtein RecA / 0.686
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.686
4goj GNPADP-ribosylation factor-like protein 3 / 0.685
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.684
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.684
5cyo GDPSeptin-9 / 0.684
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.682
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.682
3qbt GNPRas-related protein Rab-8A / 0.682
4uj5 GNPRas-related protein Rab-11A / 0.681
5di3 GNPADP-ribosylation factor-like protein 3 / 0.681
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.681
1zc4 GNPRas-related protein Ral-A / 0.680
3tjz GNPADP-ribosylation factor 1 / 0.680
1zc3 GNPRas-related protein Ral-A / 0.679
2g1q ADPKinesin-like protein KIF11 / 0.679
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.679
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.678
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.678
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.678
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.678
1r6t TYMTryptophan--tRNA ligase, cytoplasmic 6.1.1.2 0.677
1s1c GNPTransforming protein RhoA / 0.677
2uz3 TTPThymidine kinase / 0.677
2zrj AGSProtein RecA / 0.677
1w5t ANPORC1-type DNA replication protein 2 / 0.676
2y65 ADPKinesin heavy chain / 0.676
3b1x GNPFerrous iron transport protein B / 0.676
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.676
1am4 GNPCell division control protein 42 homolog / 0.674
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.674
2ad5 ADPCTP synthase / 0.674
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.674
2vor ACPFolylpolyglutamate synthase / 0.674
3t1t GDPProbable gliding protein mglA / 0.673
1w5t ADPORC1-type DNA replication protein 2 / 0.672
3kz1 GSPTransforming protein RhoA / 0.672
3zia ATPATP synthase subunit alpha, mitochondrial / 0.672
1gwn GTPRho-related GTP-binding protein RhoE / 0.671
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.671
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.671
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.670
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.670
2xsz ATPRuvB-like 2 3.6.4.12 0.670
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.670
3q9l ATPSeptum site-determining protein MinD / 0.670
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.670
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.669
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.669
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.669
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.669
3ftq GNPSeptin-2 / 0.669
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.669
1ky2 GNPGTP-binding protein YPT7 / 0.668
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.668
3pcr GTPADP-ribosylation factor 6 / 0.668
4nyi GNPGTPase HRas / 0.668
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.667
2xto GDPGTPase IMAP family member 2 / 0.667
2q3f GNPRas-related GTP-binding protein D / 0.666
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.666
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.666
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.665
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.664
1z6t ADPApoptotic protease-activating factor 1 / 0.664
2qzs ADPGlycogen synthase 2.4.1.21 0.664
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.664
3rab GNPRas-related protein Rab-3A / 0.663
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.663
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.662
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.662
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
1xmv ADPProtein RecA / 0.661
4obe GDPGTPase KRas / 0.661
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.660
1mab ATPATP synthase subunit alpha, mitochondrial / 0.659
2dft ADPShikimate kinase 2.7.1.71 0.659
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.658
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.658
5hpy GDPTransforming protein RhoA / 0.658
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.657
4jjz ADPFormate--tetrahydrofolate ligase / 0.657
4x8o AP5Adenylate kinase / 0.657
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.656
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.656
3myk ANPMyosin-2 heavy chain / 0.656
4y0v GDPADP-ribosylation factor 1, putative / 0.656
4ylg GDPADP-ribosylation factor 1, putative / 0.656
3hqd ANPKinesin-like protein KIF11 / 0.655
3tkl GTPRas-related protein Rab-1A / 0.655
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.654
4nh0 ATPESX secretion system protein EccC / 0.654
4a51 ADPKinesin-like protein KIF11 / 0.653
4x8l AP5Adenylate kinase / 0.653
4dso GSPGTPase KRas / 0.651
4oi2 ADPProtein clpf-1 / 0.651
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.650
2jlr ANPGenome polyprotein 3.4.21.91 0.650
3k1j ADPATP-dependent protease Lon / 0.650
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.650