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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
3qi2 GDP Guanine nucleotide-binding protein G(i) subunit alpha-1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3qi2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 1.230
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.844
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.833
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.832
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.748
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.746
1svl ADPLarge T antigen 3.6.4 0.741
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.735
1rrg GDPADP-ribosylation factor 1 / 0.732
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.728
4ol0 GTPGTP-binding nuclear protein Ran / 0.727
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.722
3bbp GTPRas-related protein Rab-6A / 0.721
3t1t GDPProbable gliding protein mglA / 0.715
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.712
3ea5 GDPGTP-binding nuclear protein Ran / 0.707
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.705
4g01 GDPRas-related protein RABF2b / 0.704
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.697
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.696
2gil GTPRas-related protein Rab-6A / 0.695
2bbw GP5Adenylate kinase 4, mitochondrial / 0.694
1z0d GDPRas-related protein Rab-5C / 0.693
1n6m ADPProtein claret segregational / 0.692
5l3s GNPSignal recognition particle receptor FtsY / 0.692
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.691
3a58 GNPGTP-binding protein RHO1 / 0.690
1zc4 GNPRas-related protein Ral-A / 0.689
1z2c GNPRho-related GTP-binding protein RhoC / 0.686
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.686
2j7p GNPSignal recognition particle protein / 0.686
2j7p GNPSignal recognition particle receptor FtsY / 0.686
4lhv GDPRas-related protein Rab-8A / 0.686
4ncl GDPEukaryotic translation initiation factor 5B / 0.686
1yra GDPGPN-loop GTPase PAB0955 / 0.685
3tqc ADPPantothenate kinase / 0.684
3zia ATPATP synthase subunit alpha, mitochondrial / 0.684
3tnf GNPRas-related protein Rab-8A / 0.683
1loo GTPAdenylosuccinate synthetase isozyme 1 / 0.681
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.681
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.678
2bku GTPGTP-binding nuclear protein Ran / 0.677
2ql6 ADPNicotinamide riboside kinase 1 / 0.677
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.676
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
2ffq GSPRas-related protein Rab-6B / 0.676
4hi0 GDPUrease accessory protein UreG / 0.676
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.675
1n6l GTPRas-related protein Rab-5A / 0.672
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.672
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.672
4ihq ADPConserved Archaeal protein / 0.672
2fg5 GNPRas-related protein Rab-31 / 0.671
4dsn GCPGTPase KRas / 0.670
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.669
4dsu GDPGTPase KRas / 0.669
1k5d GNPGTP-binding nuclear protein Ran / 0.668
2ewv ADPTwitching motility protein PilT / 0.668
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.668
4fid GDPG protein alpha subunit, putative / 0.668
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.667
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.667
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
2d4h 5GPGuanylate-binding protein 1 / 0.667
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.667
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.667
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.665
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
1uad GNPRas-related protein Ral-A / 0.665
3r9i ADPSeptum site-determining protein MinD / 0.665
1tu3 GNPRas-related protein Rab-5A / 0.664
4lrw GDPGTPase KRas / 0.664
4obe GDPGTPase KRas / 0.664
5bn3 ADPV-type ATP synthase alpha chain / 0.664
5bn3 ADPNEQ263 / 0.664
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.663
4l8g GDPGTPase KRas / 0.663
4uj5 GNPRas-related protein Rab-11A / 0.663
5jlj GNPGTP-binding nuclear protein Ran / 0.663
1rj9 GCPSignal recognition particle receptor FtsY / 0.662
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.662
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.662
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.662
4q03 GDPGTPase KRas / 0.662
3bxz ADPProtein translocase subunit SecA / 0.661
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.661
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.660
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.660
4nyj GNPGTPase HRas / 0.660
4o2r GDPGTP-binding protein Rheb / 0.660
4q02 GDPGTPase KRas / 0.660
1xms ANPProtein RecA / 0.659
3kud GDPGTPase HRas / 0.659
3l1c ADPProtein claret segregational / 0.659
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.659
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.659
4xvq GNPGTPase HRas / 0.659
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.658
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.658
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.658
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.658
3cph GDPRas-related protein SEC4 / 0.658
4dxa GSPRas-related protein Rap-1b / 0.658
4luc GDPGTPase KRas / 0.658
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.657
3k9l GNPGTPase HRas / 0.657
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.657
4ldj GDPGTPase KRas / 0.657
4asu ADPATP synthase subunit alpha, mitochondrial / 0.656
4kvg GTPRas-related protein Rap-1A / 0.656
4o3m ADPBloom syndrome protein 3.6.4.12 0.656
4z54 GDPNeuronal-specific septin-3 / 0.656
1oix GDPRas-related protein Rab-11A / 0.655
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.655
1z0a GDPRas-related protein Rab-2A / 0.655
3law GNPRas-related protein Rab-7a / 0.655
3tso GNPRas-related protein Rab-25 / 0.655
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.655
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.654
2cl6 CAGGTPase HRas / 0.654
2dr3 ADPUPF0273 protein PH0284 / 0.654
3e5h GNPRas-related protein Rab-28 / 0.654
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.654
3q5d GDPAtlastin-1 3.6.5 0.654
1g16 GDPRas-related protein SEC4 / 0.653
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.653
2r9v ATPATP synthase subunit alpha / 0.653
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.652
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
4qfx DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.652
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.651
2fna ADPUncharacterized protein / 0.651
3kuc GDPRas-related protein Rap-1A / 0.651
3wyf GTPGTP-binding nuclear protein / 0.651
3pcr GTPADP-ribosylation factor 6 / 0.650
3tkl GTPRas-related protein Rab-1A / 0.650