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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
4wpu GDP Phosphoenolpyruvate carboxykinase [GTP]

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.872
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.765
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.755
4xsg GSPTransforming protein RhoA / 0.740
4itr GDPCell division control protein 42 homolog / 0.739
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.730
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.724
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.722
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.720
2fe4 GDPRas-related protein Rab-6B / 0.718
4dvg GSPRho family GTPase / 0.718
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.713
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.710
5fl3 ADPPili retraction protein PilT / 0.710
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.709
4lpk GDPGTPase KRas / 0.709
1cxz GSPTransforming protein RhoA / 0.704
1z0a GDPRas-related protein Rab-2A / 0.704
3kz1 GSPTransforming protein RhoA / 0.704
4o2l GTPGTP-binding protein Rheb / 0.702
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.701
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.700
2cls GTPRho-related GTP-binding protein Rho6 / 0.700
2eck ADPAdenylate kinase / 0.700
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.699
1zbd GTPRas-related protein Rab-3A / 0.699
4i1v ADPDephospho-CoA kinase / 0.699
1rrg GDPADP-ribosylation factor 1 / 0.698
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.698
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.698
4d0l GSPRas-related protein Rab-11A / 0.697
4ike ADPAdenylate kinase / 0.696
4qm6 GTPMetallophosphoesterase / 0.696
4dso GSPGTPase KRas / 0.695
4q02 GDPGTPase KRas / 0.695
4q03 GDPGTPase KRas / 0.694
4lhv GDPRas-related protein Rab-8A / 0.693
1m7b GTPRho-related GTP-binding protein RhoE / 0.691
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.691
1t91 GTPRas-related protein Rab-7a / 0.690
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.689
3a6p GTPGTP-binding nuclear protein Ran / 0.689
5ftc ADPTPR domain protein / 0.689
1g16 GDPRas-related protein SEC4 / 0.688
4o2r GDPGTP-binding protein Rheb / 0.688
4uj3 GNPRas-related protein Rab-11A / 0.688
4wa7 GDPGTPase KRas / 0.688
1kmq GNPTransforming protein RhoA / 0.687
2ce2 GDPGTPase HRas / 0.687
3tlx ADPAdenylate kinase 2 / 0.687
1z0f GDPRas-related protein Rab-14 / 0.686
4jky ADPAdenylate kinase / 0.686
1b7t ADPMyosin heavy chain, striated muscle / 0.685
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.685
4gp6 ADPMetallophosphoesterase / 0.685
1mma ADPMyosin-2 heavy chain / 0.684
4pjk ADPMyosin-2 heavy chain / 0.684
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.683
4d81 ADPAAA ATPase, central domain protein / 0.683
4g01 GDPRas-related protein RABF2b / 0.683
1jx2 ADPMyosin-2 heavy chain / 0.682
1wdt GTPElongation factor G (EF-G-2) / 0.682
2ffq GSPRas-related protein Rab-6B / 0.682
4jl5 ADPAdenylate kinase / 0.682
4k81 GTPGTPase HRas / 0.682
4qxa GTPRas-related protein Rab-9A / 0.682
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.681
2j5x GSPADP-ribosylation factor 6 / 0.681
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.681
4pk4 ADPUnconventional myosin-VI / 0.681
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.680
2dpx GDPGTP-binding protein RAD / 0.680
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.680
3bbp GTPRas-related protein Rab-6A / 0.680
4yqf GDPSeptin-9 / 0.680
1zc3 GNPRas-related protein Ral-A / 0.678
2c9o ADPRuvB-like 1 3.6.4.12 0.678
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.678
5c46 GSPRas-related protein Rab-11A / 0.678
1mmg AGSMyosin-2 heavy chain / 0.677
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.677
3d8b ADPFidgetin-like protein 1 3.6.4 0.677
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.676
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
3x1w GDPRas-related protein Rap-1b / 0.676
2gcp GSPRho-related GTP-binding protein RhoC / 0.675
4dsu GDPGTPase KRas / 0.675
4epw GDPGTPase KRas / 0.675
4l9s GDPGTPase HRas / 0.675
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.674
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.674
2fna ADPUncharacterized protein / 0.674
4epx GDPGTPase KRas / 0.674
1x1r GDPRas-related protein M-Ras / 0.673
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.673
2vf7 ADPUvrABC system protein A / 0.673
3cph GDPRas-related protein SEC4 / 0.673
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.673
3law GNPRas-related protein Rab-7a / 0.673
4lv6 GDPGTPase KRas / 0.673
4tq9 GDPGTPase KRas / 0.673
1z2a GDPRas-related protein Rab-23 / 0.672
2fl2 ADPKinesin-like protein KIF11 / 0.672
2uyi ADPKinesin-like protein KIF11 / 0.672
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.671
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
1xtr GNPGTP-binding protein Rheb / 0.671
1yra GDPGPN-loop GTPase PAB0955 / 0.671
2ql6 ADPNicotinamide riboside kinase 1 / 0.671
4b7b ADPKinesin-like protein KIF11 / 0.671
4obe GDPGTPase KRas / 0.671
2bku GTPGTP-binding nuclear protein Ran / 0.670
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.670
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.670
3w3z GTPGTP-binding nuclear protein Ran / 0.670
4luc GDPGTPase KRas / 0.670
4o25 GTPGTP-binding protein Rheb / 0.670
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.670
4xoi GTPTransforming protein RhoA / 0.670
4asu ADPATP synthase subunit alpha, mitochondrial / 0.669
4cf7 ADPAdenylate kinase / 0.669
2gil GTPRas-related protein Rab-6A / 0.668
4mit GTPRho-related protein racC / 0.668
4pfp ADPUnconventional myosin-VI / 0.668
4ww4 ADPRuvB-like helicase / 0.668
3ref GDPRho family GTPase / 0.667
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.667
4jld ADPAdenylate kinase / 0.667
4jsy GTPMetallophosphoesterase / 0.667
4ol0 GTPGTP-binding nuclear protein Ran / 0.667
4v02 ATPSite-determining protein / 0.667
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.666
3ddc GNPGTPase HRas / 0.666
3e5h GNPRas-related protein Rab-28 / 0.666
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.666
3q5d GDPAtlastin-1 3.6.5 0.666
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
3a58 GNPGTP-binding protein RHO1 / 0.665
3k1j ADPATP-dependent protease Lon / 0.665
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.664
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.664
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.664
3wyf GTPGTP-binding nuclear protein / 0.664
1uad GNPRas-related protein Ral-A / 0.663
4lrw GDPGTPase KRas / 0.663
5bn3 ADPV-type ATP synthase alpha chain / 0.663
5bn3 ADPNEQ263 / 0.663
1w5t ANPORC1-type DNA replication protein 2 / 0.662
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.661
3q9l ATPSeptum site-determining protein MinD / 0.661
4ql3 GDPGTPase KRas / 0.661
2qen ADPWalker-Type ATPase / 0.660
3oes GNPGTPase RhebL1 / 0.660
4dlz GNPGTPase HRas / 0.660
4ldj GDPGTPase KRas / 0.660
1svw GTPProbable GTP-binding protein EngB / 0.658
3kkq GDPRas-related protein M-Ras / 0.658
4l8g GDPGTPase KRas / 0.658
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.657
4jlo ADPAdenylate kinase / 0.657
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.656
2x2r ADPKinesin-like protein KIF11 / 0.656
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.656
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.656
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.656
1gwn GTPRho-related GTP-binding protein RhoE / 0.655
2cl6 CAGGTPase HRas / 0.655
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.655
2pg2 ADPKinesin-like protein KIF11 / 0.655
1tu3 GNPRas-related protein Rab-5A / 0.654
2c5l GTPGTPase HRas / 0.654
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.654
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.654
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.653
3ea5 GDPGTP-binding nuclear protein Ran / 0.653
3l9h ADPKinesin-like protein KIF11 / 0.653
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.653
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.652
3tkl GTPRas-related protein Rab-1A / 0.652
4jl6 ADPAdenylate kinase / 0.652
5cyo GDPSeptin-9 / 0.652
1yrs ADPKinesin-like protein KIF11 / 0.651
3nbz GTPGTP-binding nuclear protein Ran / 0.651
3r9i ADPSeptum site-determining protein MinD / 0.651
3zia ATPATP synthase subunit alpha, mitochondrial / 0.651
4y0v GDPADP-ribosylation factor 1, putative / 0.651
4ylg GDPADP-ribosylation factor 1, putative / 0.651
1a2b GSPTransforming protein RhoA / 0.650
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.650
1n6l GTPRas-related protein Rab-5A / 0.650
2dft ADPShikimate kinase 2.7.1.71 0.650
2r9v ATPATP synthase subunit alpha / 0.650