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
1mez GDP Adenylosuccinate synthetase isozyme 1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1mez GDPAdenylosuccinate synthetase isozyme 1 / 1.035
1mf0 GDPAdenylosuccinate synthetase isozyme 1 / 0.936
1dj3 GDPAdenylosuccinate synthetase, chloroplastic / 0.820
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.758
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.733
1dj2 GDPAdenylosuccinate synthetase, chloroplastic / 0.732
2j7p GNPSignal recognition particle protein / 0.731
2j7p GNPSignal recognition particle receptor FtsY / 0.731
1okk GCPSignal recognition particle protein / 0.728
1okk GCPSignal recognition particle receptor FtsY / 0.728
1loo GTPAdenylosuccinate synthetase isozyme 1 / 0.718
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.718
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.718
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.718
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.716
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.716
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.716
4pfp ADPUnconventional myosin-VI / 0.716
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.715
4ql3 GDPGTPase KRas / 0.715
4d81 ADPAAA ATPase, central domain protein / 0.714
4ldj GDPGTPase KRas / 0.714
4pjj ADPUnconventional myosin-VI / 0.714
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.712
4epx GDPGTPase KRas / 0.705
4lrw GDPGTPase KRas / 0.705
1jx2 ADPMyosin-2 heavy chain / 0.704
4lpk GDPGTPase KRas / 0.704
2xae ADPKinesin-like protein KIF11 / 0.703
2zfi ADPKinesin-like protein KIF1A / 0.703
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.701
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.701
1mma ADPMyosin-2 heavy chain / 0.701
2dpx GDPGTP-binding protein RAD / 0.699
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.698
3kkq GDPRas-related protein M-Ras / 0.698
4lv6 GDPGTPase KRas / 0.697
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.696
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.696
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.695
1z0f GDPRas-related protein Rab-14 / 0.694
4xvq GNPGTPase HRas / 0.694
2y65 ADPKinesin heavy chain / 0.692
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.692
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.691
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.690
4b7b ADPKinesin-like protein KIF11 / 0.690
4luc GDPGTPase KRas / 0.690
1a2b GSPTransforming protein RhoA / 0.689
3kuc GDPRas-related protein Rap-1A / 0.689
3x1w GDPRas-related protein Rap-1b / 0.689
4pjk ADPMyosin-2 heavy chain / 0.689
1sdm ADPKinesin heavy chain-like protein / 0.688
2pg2 ADPKinesin-like protein KIF11 / 0.688
3l1c ADPProtein claret segregational / 0.688
2uyi ADPKinesin-like protein KIF11 / 0.687
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.687
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.687
4hse ADPChaperone protein ClpB / 0.687
1l8q ADPChromosomal replication initiator protein DnaA / 0.686
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.686
4dsu GDPGTPase KRas / 0.686
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.685
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.685
3tlx ADPAdenylate kinase 2 / 0.685
3k1j ADPATP-dependent protease Lon / 0.684
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
4goj GNPADP-ribosylation factor-like protein 3 / 0.682
4itr GDPCell division control protein 42 homolog / 0.682
4lhw GNPRas-related protein Rab-8A / 0.682
4hdq GNPRas-related protein Rap-1b / 0.681
3r9i ADPSeptum site-determining protein MinD / 0.680
4jky ADPAdenylate kinase / 0.680
1fnn ADPORC1-type DNA replication protein / 0.679
1jjt BDSBeta-lactamase / 0.679
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.679
4o2l GTPGTP-binding protein Rheb / 0.679
4q03 GDPGTPase KRas / 0.679
5aun ADPIron-sulfur cluster carrier protein / 0.679
3ieu GDPGTPase Era / 0.678
3mjh GTPRas-related protein Rab-5A / 0.678
2q3f GNPRas-related GTP-binding protein D / 0.677
3kud GDPGTPase HRas / 0.677
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.677
4jlo ADPAdenylate kinase / 0.677
4qos ADPPsp operon transcriptional activator / 0.677
1kqm ANPMyosin heavy chain, striated muscle / 0.676
1m7b GTPRho-related GTP-binding protein RhoE / 0.676
1uad GNPRas-related protein Ral-A / 0.676
1z0a GDPRas-related protein Rab-2A / 0.676
2vf7 ADPUvrABC system protein A / 0.676
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.676
4hi0 GDPUrease accessory protein UreG / 0.676
4jld ADPAdenylate kinase / 0.676
4o25 GTPGTP-binding protein Rheb / 0.676
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.675
1oix GDPRas-related protein Rab-11A / 0.674
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.674
3k9l GNPGTPase HRas / 0.674
3l9h ADPKinesin-like protein KIF11 / 0.674
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.673
1kmq GNPTransforming protein RhoA / 0.673
1wa5 GTPGTP-binding nuclear protein Ran / 0.673
2x2r ADPKinesin-like protein KIF11 / 0.673
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.672
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
1g16 GDPRas-related protein SEC4 / 0.671
3tqc ADPPantothenate kinase / 0.671
4l8g GDPGTPase KRas / 0.670
4obe GDPGTPase KRas / 0.670
4tq9 GDPGTPase KRas / 0.670
3i3s GNPGTPase HRas / 0.669
3oiu GNPGTPase HRas / 0.669
4g01 GDPRas-related protein RABF2b / 0.669
4g0n GNPGTPase HRas / 0.669
4l9s GDPGTPase HRas / 0.669
5l3s GNPSignal recognition particle receptor FtsY / 0.669
2fl2 ADPKinesin-like protein KIF11 / 0.668
3oiw GNPGTPase HRas / 0.668
3rs0 GNPGTPase HRas / 0.668
3rs5 GNPGTPase HRas / 0.668
3rs7 GNPGTPase HRas / 0.668
3v4f GNPGTPase HRas / 0.668
3x1z GNPRas-related protein Rap-1b / 0.668
4dlt GNPGTPase HRas / 0.668
4epw GDPGTPase KRas / 0.668
2g1q ADPKinesin-like protein KIF11 / 0.667
2rgb GNPGTPase HRas / 0.667
2x7e ADPKinesin-like protein KIF11 / 0.667
4dls GNPGTPase HRas / 0.667
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.666
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.666
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.666
3lbn GNPGTPase HRas / 0.666
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.666
4a1z ADPKinesin-like protein KIF11 / 0.666
4fvr ATPTyrosine-protein kinase JAK2 / 0.666
5di3 GNPADP-ribosylation factor-like protein 3 / 0.666
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.665
3qbt GNPRas-related protein Rab-8A / 0.665
3tjz GNPADP-ribosylation factor 1 / 0.665
4d0l GSPRas-related protein Rab-11A / 0.665
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.664
3k8y GNPGTPase HRas / 0.664
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.664
1xtr GNPGTP-binding protein Rheb / 0.663
2cea ADPATP-dependent zinc metalloprotease FtsH / 0.663
2gqr ADPPhosphoribosylaminoimidazole-succinocarboxamide synthase 6.3.2.6 0.662
2hld ANPATP synthase subunit alpha, mitochondrial / 0.662
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
3ddc GNPGTPase HRas / 0.662
3wt0 ATPCell division protein FtsA / 0.662
4q02 GDPGTPase KRas / 0.662
3tgp GNPGTPase HRas / 0.661
1tu3 GNPRas-related protein Rab-5A / 0.660
3rv3 ADPBiotin carboxylase 6.3.4.14 0.660
4ffb GTPTubulin alpha-1 chain / 0.660
1mab ATPATP synthase subunit alpha, mitochondrial / 0.659
3ea0 ATPATPase, ParA family / 0.659
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.659
3lbh GNPGTPase HRas / 0.658
4iij GTPTubulin alpha-1B chain / 0.658
4mkh AP5Adenylate kinase / 0.658
2qen ADPWalker-Type ATPase / 0.657
3ryh GTPTubulin alpha chain / 0.657
3tso GNPRas-related protein Rab-25 / 0.657
4dsc A8SAbscisic acid receptor PYL3 / 0.657
4fvq ATPTyrosine-protein kinase JAK2 / 0.657
4h5d YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.657
3pit GNPRas-related protein M-Ras / 0.656
3t1t GDPProbable gliding protein mglA / 0.656
4z54 GDPNeuronal-specific septin-3 / 0.655
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.654
2zr9 DTPProtein RecA / 0.654
3law GNPRas-related protein Rab-7a / 0.654
3oiv GNPGTPase HRas / 0.654
4db1 ANPMyosin-7 / 0.654
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.654
4o6n CDPUncharacterized protein / 0.654
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.653
2a84 ATPPantothenate synthetase 6.3.2.1 0.653
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.653
3rsl GNPGTPase HRas / 0.653
4dlv GNPGTPase HRas / 0.653
4l2x YL2Farnesyl pyrophosphate synthase 2.5.1.10 0.653
1z2c GNPRho-related GTP-binding protein RhoC / 0.652
2j5x GSPADP-ribosylation factor 6 / 0.652
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.652
3myk ANPMyosin-2 heavy chain / 0.652
4dlw GNPGTPase HRas / 0.652
4l9w GNPGTPase HRas / 0.652
5itz GTPTubulin alpha-1B chain / 0.652
1w5t ADPORC1-type DNA replication protein 2 / 0.651
1yu9 GNPRas-related protein Rab-4A / 0.651
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.651
3lbi GNPGTPase HRas / 0.651
3m0e ATPTranscriptional regulator (NtrC family) / 0.651
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.651
4asu ADPATP synthase subunit alpha, mitochondrial / 0.651
4js0 GNPCell division control protein 42 homolog / 0.651
4o4l GTPTubulin alpha-1B chain / 0.651
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.650
1zxm ANPDNA topoisomerase 2-alpha 5.99.1.3 0.650
3dzd ADPTranscriptional regulator (NtrC family) / 0.650
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.650