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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
1m2o GNP Small COPII coat GTPase SAR1 3.6.5

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 1.115
1xts GTPGTP-binding protein Rheb / 0.866
1ibr GNPGTP-binding nuclear protein Ran / 0.841
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.834
3i3s GNPGTPase HRas / 0.819
3k8y GNPGTPase HRas / 0.819
1xtr GNPGTP-binding protein Rheb / 0.816
5jlj GNPGTP-binding nuclear protein Ran / 0.815
1zc3 GNPRas-related protein Ral-A / 0.810
1wa5 GTPGTP-binding nuclear protein Ran / 0.807
3kko GNPRas-related protein M-Ras / 0.807
4lhw GNPRas-related protein Rab-8A / 0.802
5c46 GSPRas-related protein Rab-11A / 0.801
3rab GNPRas-related protein Rab-3A / 0.799
5dha GNPGTP-binding nuclear protein Ran / 0.797
3mjh GTPRas-related protein Rab-5A / 0.792
3w3z GTPGTP-binding nuclear protein Ran / 0.792
4js0 GNPCell division control protein 42 homolog / 0.792
1zc4 GNPRas-related protein Ral-A / 0.791
3ftq GNPSeptin-2 / 0.787
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.786
3x1z GNPRas-related protein Rap-1b / 0.786
4dlw GNPGTPase HRas / 0.786
2jlr ANPGenome polyprotein 3.4.21.91 0.784
3l8y GNPGTPase HRas / 0.783
2bku GTPGTP-binding nuclear protein Ran / 0.781
2c5l GTPGTPase HRas / 0.781
3lbi GNPGTPase HRas / 0.780
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.779
3pit GNPRas-related protein M-Ras / 0.779
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.777
3lbh GNPGTPase HRas / 0.776
4nyj GNPGTPase HRas / 0.775
1n6l GTPRas-related protein Rab-5A / 0.772
4g0n GNPGTPase HRas / 0.772
1kmq GNPTransforming protein RhoA / 0.771
3rs0 GNPGTPase HRas / 0.771
3rsl GNPGTPase HRas / 0.771
4l9w GNPGTPase HRas / 0.771
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.770
3lbn GNPGTPase HRas / 0.770
2gcp GSPRho-related GTP-binding protein RhoC / 0.769
2j7p GNPSignal recognition particle protein / 0.769
2j7p GNPSignal recognition particle receptor FtsY / 0.769
2rge GNPGTPase HRas / 0.767
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.766
3a58 GNPGTP-binding protein RHO1 / 0.765
4xoi GTPTransforming protein RhoA / 0.765
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.763
3oiw GNPGTPase HRas / 0.762
1s1c GNPTransforming protein RhoA / 0.761
1tu3 GNPRas-related protein Rab-5A / 0.761
4hdo GNPRas-related protein Rap-1b / 0.760
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.758
5dif GNPGTP-binding nuclear protein Ran / 0.758
3ddc GNPGTPase HRas / 0.757
5l3s GNPSignal recognition particle receptor FtsY / 0.757
2cls GTPRho-related GTP-binding protein Rho6 / 0.754
1a2b GSPTransforming protein RhoA / 0.753
2fg5 GNPRas-related protein Rab-31 / 0.753
4nyi GNPGTPase HRas / 0.753
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.750
3k9l GNPGTPase HRas / 0.750
3rs4 GNPGTPase HRas / 0.750
3rs5 GNPGTPase HRas / 0.750
3rs7 GNPGTPase HRas / 0.750
4dlx GNPGTPase HRas / 0.750
4xvq GNPGTPase HRas / 0.750
2q3f GNPRas-related GTP-binding protein D / 0.749
3vhx GTPADP-ribosylation factor 6 / 0.749
1z2c GNPRho-related GTP-binding protein RhoC / 0.748
1cxz GSPTransforming protein RhoA / 0.747
2rgb GNPGTPase HRas / 0.747
4dlz GNPGTPase HRas / 0.746
1rj9 GCPSignal recognition particle receptor FtsY / 0.745
2rgc GNPGTPase HRas / 0.745
1okk GCPSignal recognition particle protein / 0.743
1okk GCPSignal recognition particle receptor FtsY / 0.743
3eg5 GNPCell division control protein 42 homolog / 0.742
3e5h GNPRas-related protein Rab-28 / 0.741
4qxa GTPRas-related protein Rab-9A / 0.740
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.739
2gil GTPRas-related protein Rab-6A / 0.738
3oes GNPGTPase RhebL1 / 0.738
3tkl GTPRas-related protein Rab-1A / 0.738
4idn GNPAtlastin-1 3.6.5 0.738
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.737
1zbd GTPRas-related protein Rab-3A / 0.736
1yzq GNPRas-related protein Rab-6A / 0.735
3bc1 GNPRas-related protein Rab-27A / 0.735
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.735
4kvg GTPRas-related protein Rap-1A / 0.735
4rkf GNPRas-related protein Rab-3 / 0.735
2ffq GSPRas-related protein Rab-6B / 0.734
3r9x GNPGTPase Era / 0.734
1ky2 GNPGTP-binding protein YPT7 / 0.733
4qm6 GTPMetallophosphoesterase / 0.733
3b1x GNPFerrous iron transport protein B / 0.732
4dlv GNPGTPase HRas / 0.731
4idp GNPAtlastin-1 3.6.5 0.731
4o25 GTPGTP-binding protein Rheb / 0.731
4dlt GNPGTPase HRas / 0.730
5b2z GNPGTPase HRas / 0.730
1lfd GNPGTPase HRas / 0.729
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.729
1g17 GNPRas-related protein SEC4 / 0.728
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.727
1yu9 GNPRas-related protein Rab-4A / 0.727
3bbp GTPRas-related protein Rab-6A / 0.727
1z0d GDPRas-related protein Rab-5C / 0.726
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.725
3oiu GNPGTPase HRas / 0.725
3v4f GNPGTPase HRas / 0.725
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.725
4goj GNPADP-ribosylation factor-like protein 3 / 0.724
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.723
1uad GNPRas-related protein Ral-A / 0.721
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.721
3oiv GNPGTPase HRas / 0.721
3tso GNPRas-related protein Rab-25 / 0.720
4dls GNPGTPase HRas / 0.720
4xsg GSPTransforming protein RhoA / 0.720
1t91 GTPRas-related protein Rab-7a / 0.719
3nbz GTPGTP-binding nuclear protein Ran / 0.719
3tjz GNPADP-ribosylation factor 1 / 0.719
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.717
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.717
3tgp GNPGTPase HRas / 0.717
3wyf GTPGTP-binding nuclear protein / 0.717
1sq5 ADPPantothenate kinase 2.7.1.33 0.716
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.716
3m0e ATPTranscriptional regulator (NtrC family) / 0.716
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.716
4dvg GSPRho family GTPase / 0.716
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.716
4mit GTPRho-related protein racC / 0.715
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.712
5k5z ANPUncharacterized protein / 0.712
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.711
2zr9 DTPProtein RecA / 0.711
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.711
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.710
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.710
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.710
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.709
2bme GNPRas-related protein Rab-4A / 0.709
3oee ANPATP synthase subunit alpha, mitochondrial / 0.707
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.707
3zia ATPATP synthase subunit alpha, mitochondrial / 0.707
4jld ADPAdenylate kinase / 0.707
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.706
4ike ADPAdenylate kinase / 0.706
4jl5 ADPAdenylate kinase / 0.706
1f5n GNPGuanylate-binding protein 1 / 0.705
1k5d GNPGTP-binding nuclear protein Ran / 0.705
1oe0 TTPDeoxynucleoside kinase / 0.705
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.703
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.703
4nh0 ATPESX secretion system protein EccC / 0.702
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.702
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.701
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.700
1am4 GNPCell division control protein 42 homolog / 0.699
3tqc ADPPantothenate kinase / 0.699
5di3 GNPADP-ribosylation factor-like protein 3 / 0.699
2bc9 GNPGuanylate-binding protein 1 / 0.698
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
3r9i ADPSeptum site-determining protein MinD / 0.698
1oix GDPRas-related protein Rab-11A / 0.697
1v8k ANPKinesin-like protein KIF2C / 0.697
3thy ADPDNA mismatch repair protein Msh2 / 0.697
4dsn GCPGTPase KRas / 0.697
4jsy GTPMetallophosphoesterase / 0.697
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.697
2c96 ATPPsp operon transcriptional activator / 0.696
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.696
3kz1 GSPTransforming protein RhoA / 0.696
5fl3 ADPPili retraction protein PilT / 0.695
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.695
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.694
1yra GDPGPN-loop GTPase PAB0955 / 0.694
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.694
1g16 GDPRas-related protein SEC4 / 0.692
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.692
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.691
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.690
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
1z6t ADPApoptotic protease-activating factor 1 / 0.690
4itr GDPCell division control protein 42 homolog / 0.690
4v02 ATPSite-determining protein / 0.690
1z0f GDPRas-related protein Rab-14 / 0.689
2qen ADPWalker-Type ATPase / 0.689
3qbt GNPRas-related protein Rab-8A / 0.689
4ncl GDPEukaryotic translation initiation factor 5B / 0.689
2gm1 ADPKinesin-like protein KIF11 / 0.688
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.688
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.688
4lpk GDPGTPase KRas / 0.688
1mmg AGSMyosin-2 heavy chain / 0.687
1w5t ANPORC1-type DNA replication protein 2 / 0.687
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.687
4hdq GNPRas-related protein Rap-1b / 0.687
4i1v ADPDephospho-CoA kinase / 0.686
2ce2 GDPGTPase HRas / 0.685
3t1t GDPProbable gliding protein mglA / 0.685
4hse ADPChaperone protein ClpB / 0.685
1d5c GDPGTPase (Rab6) / 0.684
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.684
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.684
1l8q ADPChromosomal replication initiator protein DnaA / 0.684
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.684
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.683
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.683
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.683
4o2r GDPGTP-binding protein Rheb / 0.683
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.681
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.681
4k81 GTPGTPase HRas / 0.681
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.680
2fe4 GDPRas-related protein Rab-6B / 0.680
4asu ADPATP synthase subunit alpha, mitochondrial / 0.680
2bbw GP5Adenylate kinase 4, mitochondrial / 0.679
5d3q GDPDynamin-1 3.6.5.5 0.679
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.678
4g01 GDPRas-related protein RABF2b / 0.677
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.677
1ny5 ADPTranscriptional regulator (NtrC family) / 0.676
2r9v ATPATP synthase subunit alpha / 0.676
3myk ANPMyosin-2 heavy chain / 0.676
4lhv GDPRas-related protein Rab-8A / 0.676
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.676
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.674
3dm5 GDPSignal recognition particle 54 kDa protein / 0.674
1wdt GTPElongation factor G (EF-G-2) / 0.673
4d81 ADPAAA ATPase, central domain protein / 0.672
4pjk ADPMyosin-2 heavy chain / 0.672
2zet GTPRas-related protein Rab-27B / 0.671
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.671
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.671
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.670
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.670
1svw GTPProbable GTP-binding protein EngB / 0.670
1wbb ADPDNA mismatch repair protein MutS / 0.670
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.670
1fnn ADPORC1-type DNA replication protein / 0.669
4ihq ADPConserved Archaeal protein / 0.669
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
1vg8 GNPRas-related protein Rab-7a / 0.668
3cph GDPRas-related protein SEC4 / 0.667
4ql3 GDPGTPase KRas / 0.667
4y0v GDPADP-ribosylation factor 1, putative / 0.667
4ylg GDPADP-ribosylation factor 1, putative / 0.667
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.665
4qnr ATPPsp operon transcriptional activator / 0.665
2c9o ADPRuvB-like 1 3.6.4.12 0.664
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.664
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.664
4cid ANPEH domain-containing protein 2 / 0.664
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.664
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.663
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.663
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
2y65 ADPKinesin heavy chain / 0.663
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
2dpx GDPGTP-binding protein RAD / 0.662
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.662
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.662
4cym GCPRas-related protein Rab-32 / 0.662
3d8b ADPFidgetin-like protein 1 3.6.4 0.661
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.661
1jx2 ADPMyosin-2 heavy chain / 0.660
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
2fna ADPUncharacterized protein / 0.660
2r6g ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.660
3a6p GTPGTP-binding nuclear protein Ran / 0.660
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.660
4z54 GDPNeuronal-specific septin-3 / 0.660
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.659
2zrj AGSProtein RecA / 0.659
3l9h ADPKinesin-like protein KIF11 / 0.659
3zfd ANPChromosome-associated kinesin KIF4 / 0.659
4dso GSPGTPase KRas / 0.659
4jlo ADPAdenylate kinase / 0.659
4qbg AP5Adenylate kinase / 0.659
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.659
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.658
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
2a5y ATPCell death protein 4 / 0.658
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.658
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.658
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.658
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.658
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.657
1kqm ANPMyosin heavy chain, striated muscle / 0.657
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.657
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.657
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.657
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.657
1svm ATPLarge T antigen 3.6.4 0.656
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.656
3k1j ADPATP-dependent protease Lon / 0.656
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.655
1ow3 GDPTransforming protein RhoA / 0.655
2hld ANPATP synthase subunit alpha, mitochondrial / 0.655
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
4iok ADPFormate--tetrahydrofolate ligase / 0.655
1ank ANPAdenylate kinase / 0.654
1g41 ADPATP-dependent protease ATPase subunit HslU / 0.654
1z2a GDPRas-related protein Rab-23 / 0.654
4cf7 ADPAdenylate kinase / 0.654
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.654
4xvu ATPATPase GET3 / 0.654
2vos ADPFolylpolyglutamate synthase / 0.653
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.653
1xmv ADPProtein RecA / 0.652
1g6o ADPCag alpha / 0.651
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.651
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.651
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.651
3ea5 GDPGTP-binding nuclear protein Ran / 0.651
3kuc GDPRas-related protein Rap-1A / 0.651
3qi2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.651
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.650
2c9c ATPPsp operon transcriptional activator / 0.650
3hqd ANPKinesin-like protein KIF11 / 0.650
4wa7 GDPGTPase KRas / 0.650