Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3ea0 ATP ATPase, ParA family

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3ea0 ATPATPase, ParA family / 1.171
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.768
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.767
4lhv GDPRas-related protein Rab-8A / 0.753
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.749
3kuc GDPRas-related protein Rap-1A / 0.745
4ys0 ADPProtein translocase subunit SecA / 0.744
3mjh GTPRas-related protein Rab-5A / 0.743
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.742
2ffq GSPRas-related protein Rab-6B / 0.741
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.731
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.730
3kud GDPGTPase HRas / 0.730
1d5c GDPGTPase (Rab6) / 0.729
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.728
4epx GDPGTPase KRas / 0.728
3vhx GTPADP-ribosylation factor 6 / 0.727
2j5x GSPADP-ribosylation factor 6 / 0.725
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.725
4rz3 ADPSite-determining protein / 0.725
1x1r GDPRas-related protein M-Ras / 0.724
3pcr GTPADP-ribosylation factor 6 / 0.724
4g0n GNPGTPase HRas / 0.724
2bku GTPGTP-binding nuclear protein Ran / 0.723
4jld ADPAdenylate kinase / 0.722
3t1t GDPProbable gliding protein mglA / 0.717
4l8g GDPGTPase KRas / 0.717
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.716
3ieu GDPGTPase Era / 0.716
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.715
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.715
4l9s GDPGTPase HRas / 0.715
4lv6 GDPGTPase KRas / 0.715
4pjk ADPMyosin-2 heavy chain / 0.715
4y0v GDPADP-ribosylation factor 1, putative / 0.715
2fe4 GDPRas-related protein Rab-6B / 0.714
3x1w GDPRas-related protein Rap-1b / 0.714
4q03 GDPGTPase KRas / 0.714
4ql3 GDPGTPase KRas / 0.714
4tq9 GDPGTPase KRas / 0.714
4wa7 GDPGTPase KRas / 0.714
4ylg GDPADP-ribosylation factor 1, putative / 0.714
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.713
1rrg GDPADP-ribosylation factor 1 / 0.713
4dso GSPGTPase KRas / 0.712
4dsu GDPGTPase KRas / 0.712
4v02 ATPSite-determining protein / 0.712
1z2a GDPRas-related protein Rab-23 / 0.711
3tqc ADPPantothenate kinase / 0.711
4jky ADPAdenylate kinase / 0.711
4pfp ADPUnconventional myosin-VI / 0.711
1ibr GNPGTP-binding nuclear protein Ran / 0.710
1sq5 ADPPantothenate kinase 2.7.1.33 0.710
4cf7 ADPAdenylate kinase / 0.710
4o2l GTPGTP-binding protein Rheb / 0.710
4xvq GNPGTPase HRas / 0.709
4b7b ADPKinesin-like protein KIF11 / 0.708
4cym GCPRas-related protein Rab-32 / 0.708
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.707
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.706
4jlo ADPAdenylate kinase / 0.706
3kkq GDPRas-related protein M-Ras / 0.702
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.701
1oix GDPRas-related protein Rab-11A / 0.700
2bme GNPRas-related protein Rab-4A / 0.700
4a28 ADPKinesin-like protein KIF11 / 0.699
4q02 GDPGTPase KRas / 0.699
3cob ADPKinesin heavy chain-like protein / 0.698
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.697
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.697
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.697
3ez6 ADPPlasmid partition protein A / 0.697
3tgp GNPGTPase HRas / 0.697
4k81 GTPGTPase HRas / 0.697
4ike ADPAdenylate kinase / 0.696
4o2r GDPGTP-binding protein Rheb / 0.696
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.695
2ce2 GDPGTPase HRas / 0.695
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.695
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.694
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.694
1mma ADPMyosin-2 heavy chain / 0.694
2c98 ADPPsp operon transcriptional activator / 0.694
2xto GDPGTPase IMAP family member 2 / 0.694
3lbh GNPGTPase HRas / 0.694
3oiw GNPGTPase HRas / 0.694
3rsl GNPGTPase HRas / 0.694
3tjz GNPADP-ribosylation factor 1 / 0.694
4hdo GNPRas-related protein Rap-1b / 0.694
4jl5 ADPAdenylate kinase / 0.694
4l9w GNPGTPase HRas / 0.694
2rge GNPGTPase HRas / 0.693
3oiv GNPGTPase HRas / 0.693
1g17 GNPRas-related protein SEC4 / 0.692
3ddc GNPGTPase HRas / 0.692
3lbn GNPGTPase HRas / 0.692
4d0l GSPRas-related protein Rab-11A / 0.692
1zc4 GNPRas-related protein Ral-A / 0.691
2dpx GDPGTP-binding protein RAD / 0.691
4a1z ADPKinesin-like protein KIF11 / 0.691
4jl6 ADPAdenylate kinase / 0.691
5c46 GSPRas-related protein Rab-11A / 0.691
1w5s ADPORC1-type DNA replication protein 2 / 0.688
1wa5 GTPGTP-binding nuclear protein Ran / 0.688
3l9h ADPKinesin-like protein KIF11 / 0.688
4lhw GNPRas-related protein Rab-8A / 0.688
4xvu ATPATPase GET3 / 0.688
1ny5 ADPTranscriptional regulator (NtrC family) / 0.687
4ldj GDPGTPase KRas / 0.687
2g1q ADPKinesin-like protein KIF11 / 0.686
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.685
4epw GDPGTPase KRas / 0.685
4obe GDPGTPase KRas / 0.685
1sdm ADPKinesin heavy chain-like protein / 0.684
4lpk GDPGTPase KRas / 0.684
5bn3 ADPV-type ATP synthase alpha chain / 0.684
5bn3 ADPNEQ263 / 0.684
4lrw GDPGTPase KRas / 0.683
4luc GDPGTPase KRas / 0.683
2fl2 ADPKinesin-like protein KIF11 / 0.682
2fna ADPUncharacterized protein / 0.681
2x2r ADPKinesin-like protein KIF11 / 0.681
4kvg GTPRas-related protein Rap-1A / 0.681
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.680
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.680
1wbb ADPDNA mismatch repair protein MutS / 0.680
2uyi ADPKinesin-like protein KIF11 / 0.680
2x7e ADPKinesin-like protein KIF11 / 0.680
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.680
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.680
4pjj ADPUnconventional myosin-VI / 0.680
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.679
1uad GNPRas-related protein Ral-A / 0.679
1yra GDPGPN-loop GTPase PAB0955 / 0.679
4xvr GNPGTPase HRas / 0.679
1jx2 ADPMyosin-2 heavy chain / 0.678
2xsz ATPRuvB-like 2 3.6.4.12 0.678
4goj GNPADP-ribosylation factor-like protein 3 / 0.678
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.677
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.677
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.677
3qbt GNPRas-related protein Rab-8A / 0.677
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.676
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
2xae ADPKinesin-like protein KIF11 / 0.676
3ea5 GDPGTP-binding nuclear protein Ran / 0.676
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.675
1z6t ADPApoptotic protease-activating factor 1 / 0.675
4dzz ADPPlasmid partitioning protein ParF / 0.675
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.674
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.673
3q5d GDPAtlastin-1 3.6.5 0.673
2o8b ADPDNA mismatch repair protein Msh2 / 0.672
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.672
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.672
5aun ADPIron-sulfur cluster carrier protein / 0.672
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.671
2qen ADPWalker-Type ATPase / 0.670
2zfi ADPKinesin-like protein KIF1A / 0.670
3a37 ADPATPase GET3 / 0.670
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.668
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
4zca ADPKinesin-like protein KIF11 / 0.667
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.667
2zrj AGSProtein RecA / 0.666
2pg2 ADPKinesin-like protein KIF11 / 0.665
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.665
3cph GDPRas-related protein SEC4 / 0.665
1b7t ADPMyosin heavy chain, striated muscle / 0.664
4a51 ADPKinesin-like protein KIF11 / 0.664
1lfd GNPGTPase HRas / 0.663
3tnf GNPRas-related protein Rab-8A / 0.663
4e07 ACPPlasmid partitioning protein ParF / 0.663
4hdq GNPRas-related protein Rap-1b / 0.663
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.662
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
1z0f GDPRas-related protein Rab-14 / 0.662
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.662
4qos ADPPsp operon transcriptional activator / 0.662
1ky2 GNPGTP-binding protein YPT7 / 0.661
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.661
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.661
2rgg GNPGTPase HRas / 0.661
3r9i ADPSeptum site-determining protein MinD / 0.661
1n6l GTPRas-related protein Rab-5A / 0.660
3k1j ADPATP-dependent protease Lon / 0.660
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.659
1yrs ADPKinesin-like protein KIF11 / 0.658
2gm1 ADPKinesin-like protein KIF11 / 0.658
2j7p GNPSignal recognition particle protein / 0.658
2j7p GNPSignal recognition particle receptor FtsY / 0.658
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.658
1m7b GTPRho-related GTP-binding protein RhoE / 0.657
1r6t TYMTryptophan--tRNA ligase, cytoplasmic 6.1.1.2 0.657
1z0a GDPRas-related protein Rab-2A / 0.657
1gwn GTPRho-related GTP-binding protein RhoE / 0.656
2zet GTPRas-related protein Rab-27B / 0.656
3k3b ADPKinesin-like protein KIF11 / 0.656
4asu ADPATP synthase subunit alpha, mitochondrial / 0.656
4iok ADPFormate--tetrahydrofolate ligase / 0.656
1g16 GDPRas-related protein SEC4 / 0.655
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.655
3nbz GTPGTP-binding nuclear protein Ran / 0.655
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.655
5l3s GNPSignal recognition particle receptor FtsY / 0.655
1l8q ADPChromosomal replication initiator protein DnaA / 0.654
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.654
3dzd ADPTranscriptional regulator (NtrC family) / 0.653
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.653
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.651
4oi2 ADPProtein clpf-1 / 0.651