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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
2zrj AGS Protein RecA

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2zrj AGSProtein RecA / 0.985
2zro ADPProtein RecA / 0.847
1xp8 AGSProtein RecA / 0.822
2zr9 DTPProtein RecA / 0.805
1xmv ADPProtein RecA / 0.802
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.776
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.771
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.765
4z54 GDPNeuronal-specific septin-3 / 0.760
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.757
1w5s ADPORC1-type DNA replication protein 2 / 0.756
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.755
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.751
1wbb ADPDNA mismatch repair protein MutS / 0.751
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.750
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.749
3r9i ADPSeptum site-determining protein MinD / 0.749
3l9h ADPKinesin-like protein KIF11 / 0.748
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.747
2x2r ADPKinesin-like protein KIF11 / 0.747
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.746
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.746
1l8q ADPChromosomal replication initiator protein DnaA / 0.746
3q5d GDPAtlastin-1 3.6.5 0.745
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.744
3ieu GDPGTPase Era / 0.744
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.744
4asu ADPATP synthase subunit alpha, mitochondrial / 0.744
3pcr GTPADP-ribosylation factor 6 / 0.743
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.742
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.742
3tqc ADPPantothenate kinase / 0.741
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.741
3law GNPRas-related protein Rab-7a / 0.740
3qbv GDPCell division control protein 42 homolog / 0.740
4jky ADPAdenylate kinase / 0.740
5cyo GDPSeptin-9 / 0.740
3tlx ADPAdenylate kinase 2 / 0.738
5fl3 ADPPili retraction protein PilT / 0.738
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.737
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.737
3ea5 GDPGTP-binding nuclear protein Ran / 0.737
3vhx GTPADP-ribosylation factor 6 / 0.737
4lrw GDPGTPase KRas / 0.737
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.736
2fe4 GDPRas-related protein Rab-6B / 0.735
4b7b ADPKinesin-like protein KIF11 / 0.735
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.734
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.732
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.732
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.732
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.731
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.731
2pg2 ADPKinesin-like protein KIF11 / 0.731
2xae ADPKinesin-like protein KIF11 / 0.731
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.731
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.730
2uyi ADPKinesin-like protein KIF11 / 0.730
3k1j ADPATP-dependent protease Lon / 0.730
4dsu GDPGTPase KRas / 0.730
4ncl GDPEukaryotic translation initiation factor 5B / 0.730
4qxa GTPRas-related protein Rab-9A / 0.730
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.729
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.729
2y65 ADPKinesin heavy chain / 0.729
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.729
3cob ADPKinesin heavy chain-like protein / 0.728
3t1t GDPProbable gliding protein mglA / 0.728
1oix GDPRas-related protein Rab-11A / 0.727
1zbd GTPRas-related protein Rab-3A / 0.727
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.727
2gm1 ADPKinesin-like protein KIF11 / 0.727
2whx ADPGenome polyprotein 3.4.21.91 0.727
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.727
2zfi ADPKinesin-like protein KIF1A / 0.727
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.727
4cf7 ADPAdenylate kinase / 0.727
5bn3 ADPV-type ATP synthase alpha chain / 0.727
5bn3 ADPNEQ263 / 0.727
1jx2 ADPMyosin-2 heavy chain / 0.726
2bku GTPGTP-binding nuclear protein Ran / 0.726
4jl6 ADPAdenylate kinase / 0.726
4o2r GDPGTP-binding protein Rheb / 0.726
1d5c GDPGTPase (Rab6) / 0.725
1z2a GDPRas-related protein Rab-23 / 0.725
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.725
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.725
4jl5 ADPAdenylate kinase / 0.725
4jlo ADPAdenylate kinase / 0.725
4lpk GDPGTPase KRas / 0.725
1z0d GDPRas-related protein Rab-5C / 0.724
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.724
4cym GCPRas-related protein Rab-32 / 0.724
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.724
2o8b ADPDNA mismatch repair protein Msh2 / 0.723
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.723
2dr3 ADPUPF0273 protein PH0284 / 0.722
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.722
4dxa GSPRas-related protein Rap-1b / 0.722
4ike ADPAdenylate kinase / 0.722
4jld ADPAdenylate kinase / 0.722
4luc GDPGTPase KRas / 0.722
4y0v GDPADP-ribosylation factor 1, putative / 0.722
4ylg GDPADP-ribosylation factor 1, putative / 0.722
4a1z ADPKinesin-like protein KIF11 / 0.721
4a51 ADPKinesin-like protein KIF11 / 0.721
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.721
4nh0 ATPESX secretion system protein EccC / 0.721
1nly AGSCag alpha / 0.720
1xtr GNPGTP-binding protein Rheb / 0.719
5ftc ADPTPR domain protein / 0.718
4hi0 GDPUrease accessory protein UreG / 0.717
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.716
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.716
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.716
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.716
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.715
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.715
4ihq ADPConserved Archaeal protein / 0.715
2x7e ADPKinesin-like protein KIF11 / 0.714
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.714
1sdm ADPKinesin heavy chain-like protein / 0.713
4gp6 ADPMetallophosphoesterase / 0.713
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.712
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.712
4g0n GNPGTPase HRas / 0.712
5aun ADPIron-sulfur cluster carrier protein / 0.712
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.711
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.711
3x1w GDPRas-related protein Rap-1b / 0.711
4lv6 GDPGTPase KRas / 0.711
4tq9 GDPGTPase KRas / 0.711
4itr GDPCell division control protein 42 homolog / 0.710
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.710
1rrg GDPADP-ribosylation factor 1 / 0.709
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.709
2zts ADPUncharacterized protein / 0.709
4epx GDPGTPase KRas / 0.709
4obe GDPGTPase KRas / 0.709
1z0a GDPRas-related protein Rab-2A / 0.708
2ce2 GDPGTPase HRas / 0.708
3w3z GTPGTP-binding nuclear protein Ran / 0.708
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.708
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.707
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.707
1g6o ADPCag alpha / 0.707
1sq5 ADPPantothenate kinase 2.7.1.33 0.707
2q3f GNPRas-related GTP-binding protein D / 0.707
4ldj GDPGTPase KRas / 0.707
4qos ADPPsp operon transcriptional activator / 0.707
1mma ADPMyosin-2 heavy chain / 0.706
3cph GDPRas-related protein SEC4 / 0.706
3kud GDPGTPase HRas / 0.706
2dpx GDPGTP-binding protein RAD / 0.705
1xms ANPProtein RecA / 0.704
2ql6 ADPNicotinamide riboside kinase 1 / 0.704
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.703
1z6t ADPApoptotic protease-activating factor 1 / 0.702
2j5x GSPADP-ribosylation factor 6 / 0.702
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.702
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.701
4a28 ADPKinesin-like protein KIF11 / 0.701
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.700
1yra GDPGPN-loop GTPase PAB0955 / 0.700
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.700
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.699
2uz3 TTPThymidine kinase / 0.699
3mjh GTPRas-related protein Rab-5A / 0.699
4goj GNPADP-ribosylation factor-like protein 3 / 0.699
4q03 GDPGTPase KRas / 0.699
4zca ADPKinesin-like protein KIF11 / 0.699
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.698
2fl2 ADPKinesin-like protein KIF11 / 0.697
4yqf GDPSeptin-9 / 0.697
1ibr GNPGTP-binding nuclear protein Ran / 0.696
2eck ADPAdenylate kinase / 0.696
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.696
4iei ADPGene 2 protein / 0.696
4pk4 ADPUnconventional myosin-VI / 0.696
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.696
1k5d GNPGTP-binding nuclear protein Ran / 0.695
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.695
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.695
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
3c41 ANPAmino acid ABC transporter / 0.695
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.695
4o2l GTPGTP-binding protein Rheb / 0.695
1b7t ADPMyosin heavy chain, striated muscle / 0.694
2vf7 ADPUvrABC system protein A / 0.694
4xsg GSPTransforming protein RhoA / 0.694
4xvq GNPGTPase HRas / 0.694
4xvr GNPGTPase HRas / 0.694
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.693
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.693
4oi2 ADPProtein clpf-1 / 0.693
4ql3 GDPGTPase KRas / 0.693
1z0f GDPRas-related protein Rab-14 / 0.692
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.692
3ref GDPRho family GTPase / 0.692
3zia ATPATP synthase subunit alpha, mitochondrial / 0.692
4ww4 ADPRuvB-like helicase / 0.691
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.690
2c9c ATPPsp operon transcriptional activator / 0.690
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.690
4d81 ADPAAA ATPase, central domain protein / 0.690
1ow3 GDPTransforming protein RhoA / 0.689
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.689
2c96 ATPPsp operon transcriptional activator / 0.689
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.689
3d8b ADPFidgetin-like protein 1 3.6.4 0.689
3zfd ANPChromosome-associated kinesin KIF4 / 0.689
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.688
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.688
2c9o ADPRuvB-like 1 3.6.4.12 0.688
4js0 GNPCell division control protein 42 homolog / 0.688
1f5n GNPGuanylate-binding protein 1 / 0.687
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.687
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.687
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.687
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.686
4hse ADPChaperone protein ClpB / 0.686
4idp GNPAtlastin-1 3.6.5 0.686
5dha GNPGTP-binding nuclear protein Ran / 0.686
1ii6 ADPKinesin-like protein KIF11 / 0.685
2xsz ATPRuvB-like 2 3.6.4.12 0.685
1v8k ANPKinesin-like protein KIF2C / 0.684
2hld ANPATP synthase subunit alpha, mitochondrial / 0.682
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.682
3k3b ADPKinesin-like protein KIF11 / 0.682
3tjz GNPADP-ribosylation factor 1 / 0.682
1w5t ANPORC1-type DNA replication protein 2 / 0.681
3oee ANPATP synthase subunit alpha, mitochondrial / 0.681
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.681
3oiu GNPGTPase HRas / 0.680
5di3 GNPADP-ribosylation factor-like protein 3 / 0.680
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.679
2rge GNPGTPase HRas / 0.679
3oiw GNPGTPase HRas / 0.679
4jjz ADPFormate--tetrahydrofolate ligase / 0.679
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.678
3kz1 GSPTransforming protein RhoA / 0.678
3m0e ATPTranscriptional regulator (NtrC family) / 0.678
3rs0 GNPGTPase HRas / 0.678
3rs5 GNPGTPase HRas / 0.678
3rsl GNPGTPase HRas / 0.678
3v4f GNPGTPase HRas / 0.678
4dlw GNPGTPase HRas / 0.678
4l9w GNPGTPase HRas / 0.678
1s1c GNPTransforming protein RhoA / 0.677
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.677
4iok ADPFormate--tetrahydrofolate ligase / 0.677
4mkh AP5Adenylate kinase / 0.677
4o3m ADPBloom syndrome protein 3.6.4.12 0.677
4ys0 ADPProtein translocase subunit SecA / 0.677
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.676
1w5t ADPORC1-type DNA replication protein 2 / 0.676
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.676
4idn GNPAtlastin-1 3.6.5 0.676
5k5z ANPUncharacterized protein / 0.676
1am4 GNPCell division control protein 42 homolog / 0.675
1ky2 GNPGTP-binding protein YPT7 / 0.675
2rgb GNPGTPase HRas / 0.675
3e5h GNPRas-related protein Rab-28 / 0.675
3myk ANPMyosin-2 heavy chain / 0.675
3oiv GNPGTPase HRas / 0.675
4hdo GNPRas-related protein Rap-1b / 0.675
4rkf GNPRas-related protein Rab-3 / 0.675
1uad GNPRas-related protein Ral-A / 0.674
2bbw GP5Adenylate kinase 4, mitochondrial / 0.674
3ddc GNPGTPase HRas / 0.674
3lbh GNPGTPase HRas / 0.674
3x1z GNPRas-related protein Rap-1b / 0.674
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.674
4dlt GNPGTPase HRas / 0.674
4hdq GNPRas-related protein Rap-1b / 0.674
4lhw GNPRas-related protein Rab-8A / 0.674
1lfd GNPGTPase HRas / 0.673
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.673
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.673
2rgc GNPGTPase HRas / 0.673
3kko GNPRas-related protein M-Ras / 0.673
3lbn GNPGTPase HRas / 0.673
3pit GNPRas-related protein M-Ras / 0.673
4dlv GNPGTPase HRas / 0.673
4dlz GNPGTPase HRas / 0.673
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.672
4dlx GNPGTPase HRas / 0.672
5ftf ADPTPR domain protein / 0.671
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.670
2yeg XQGHeat shock protein HSP 90-alpha / 0.670
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.670
4uj3 GNPRas-related protein Rab-11A / 0.670
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.670
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.669
3ftq GNPSeptin-2 / 0.669
3lbi GNPGTPase HRas / 0.669
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.669
5d3q GDPDynamin-1 3.6.5.5 0.669
3l8y GNPGTPase HRas / 0.668
3qbt GNPRas-related protein Rab-8A / 0.668
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.668
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.667
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.667
3ea0 ATPATPase, ParA family / 0.666
3uk6 ADPRuvB-like 2 3.6.4.12 0.666
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.665
2dft ADPShikimate kinase 2.7.1.71 0.664
2l0x GDPGTP-binding protein Rheb / 0.664
5b2z GNPGTPase HRas / 0.664
3rs7 GNPGTPase HRas / 0.663
2r9v ATPATP synthase subunit alpha / 0.662
3b1x GNPFerrous iron transport protein B / 0.662
1svl ADPLarge T antigen 3.6.4 0.661
1zc3 GNPRas-related protein Ral-A / 0.661
1oyy AGSATP-dependent DNA helicase RecQ 3.6.4.12 0.660
2zsa ADPPantothenate kinase 2.7.1.33 0.660
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.660
3oes GNPGTPase RhebL1 / 0.660
3rs4 GNPGTPase HRas / 0.660
4o25 GTPGTP-binding protein Rheb / 0.660
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.659
4dls GNPGTPase HRas / 0.659
1z2c GNPRho-related GTP-binding protein RhoC / 0.658
1zio AP5Adenylate kinase / 0.658
1yrs ADPKinesin-like protein KIF11 / 0.657
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.657
4b8w GDPGDP-L-fucose synthase 1.1.1.271 0.657
4qnr ATPPsp operon transcriptional activator / 0.657
1p9w ANPType II secretion system protein E / 0.655
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.655
4uxj TTPThymidine kinase / 0.655
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.655
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.655
3wyf GTPGTP-binding nuclear protein / 0.654
1w7i ADPUnconventional myosin-Va / 0.653
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.652
3nbx ADPATPase RavA 3.6.3 0.652