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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
2xto GDP GTPase IMAP family member 2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2xto GDPGTPase IMAP family member 2 / 0.955
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.776
2xtn GTPGTPase IMAP family member 2 / 0.775
4lrw GDPGTPase KRas / 0.771
1d5c GDPGTPase (Rab6) / 0.758
3b1x GNPFerrous iron transport protein B / 0.757
4ncl GDPEukaryotic translation initiation factor 5B / 0.750
4g0n GNPGTPase HRas / 0.749
4lhv GDPRas-related protein Rab-8A / 0.749
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.747
2gil GTPRas-related protein Rab-6A / 0.744
3kud GDPGTPase HRas / 0.744
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.743
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.740
2ffq GSPRas-related protein Rab-6B / 0.737
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.733
5hpy GDPTransforming protein RhoA / 0.733
1oix GDPRas-related protein Rab-11A / 0.731
1tu3 GNPRas-related protein Rab-5A / 0.729
4kvg GTPRas-related protein Rap-1A / 0.729
1xts GTPGTP-binding protein Rheb / 0.728
3mjh GTPRas-related protein Rab-5A / 0.727
3a58 GNPGTP-binding protein RHO1 / 0.726
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.723
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.721
2dpx GDPGTP-binding protein RAD / 0.721
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.721
4luc GDPGTPase KRas / 0.721
5dif GNPGTP-binding nuclear protein Ran / 0.721
1ow3 GDPTransforming protein RhoA / 0.719
4y0v GDPADP-ribosylation factor 1, putative / 0.718
4ylg GDPADP-ribosylation factor 1, putative / 0.718
4ldj GDPGTPase KRas / 0.717
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.716
3tkl GTPRas-related protein Rab-1A / 0.716
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.715
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.714
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.714
2gcp GSPRho-related GTP-binding protein RhoC / 0.714
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.714
1z0d GDPRas-related protein Rab-5C / 0.713
1ibr GNPGTP-binding nuclear protein Ran / 0.712
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.712
3kuc GDPRas-related protein Rap-1A / 0.710
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.710
1xtr GNPGTP-binding protein Rheb / 0.709
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.709
3w3z GTPGTP-binding nuclear protein Ran / 0.709
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.708
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.708
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.707
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.707
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.707
1yzq GNPRas-related protein Rab-6A / 0.707
2c5l GTPGTPase HRas / 0.706
3tjz GNPADP-ribosylation factor 1 / 0.706
1wa5 GTPGTP-binding nuclear protein Ran / 0.705
4yqf GDPSeptin-9 / 0.705
2j7p GNPSignal recognition particle protein / 0.703
2j7p GNPSignal recognition particle receptor FtsY / 0.703
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.703
4qxa GTPRas-related protein Rab-9A / 0.703
1n6l GTPRas-related protein Rab-5A / 0.702
4obe GDPGTPase KRas / 0.702
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.701
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.701
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.701
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.701
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.701
4z54 GDPNeuronal-specific septin-3 / 0.701
5jlj GNPGTP-binding nuclear protein Ran / 0.700
2bku GTPGTP-binding nuclear protein Ran / 0.699
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.699
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.699
3bbp GTPRas-related protein Rab-6A / 0.699
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.699
4d0l GSPRas-related protein Rab-11A / 0.698
1a2b GSPTransforming protein RhoA / 0.697
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.697
3qbv GDPCell division control protein 42 homolog / 0.696
4lhw GNPRas-related protein Rab-8A / 0.696
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.695
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
1gwn GTPRho-related GTP-binding protein RhoE / 0.695
4k81 GTPGTPase HRas / 0.695
4o25 GTPGTP-binding protein Rheb / 0.695
1sxj AGSReplication factor C subunit 1 / 0.694
3ea0 ATPATPase, ParA family / 0.694
4pjj ADPUnconventional myosin-VI / 0.694
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.693
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.693
4cf7 ADPAdenylate kinase / 0.693
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.692
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.692
1yrs ADPKinesin-like protein KIF11 / 0.692
3x1z GNPRas-related protein Rap-1b / 0.692
3eg5 GNPCell division control protein 42 homolog / 0.691
2g1q ADPKinesin-like protein KIF11 / 0.690
3ea5 GDPGTP-binding nuclear protein Ran / 0.688
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.687
4fid GDPG protein alpha subunit, putative / 0.687
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.686
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.686
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.686
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.685
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.685
2xae ADPKinesin-like protein KIF11 / 0.685
3bc1 GNPRas-related protein Rab-27A / 0.685
3r9x GNPGTPase Era / 0.685
4dsu GDPGTPase KRas / 0.685
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.684
4dxa GSPRas-related protein Rap-1b / 0.684
1okk GCPSignal recognition particle protein / 0.683
1okk GCPSignal recognition particle receptor FtsY / 0.683
3r9i ADPSeptum site-determining protein MinD / 0.683
4qos ADPPsp operon transcriptional activator / 0.683
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.683
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.683
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.683
4xoi GTPTransforming protein RhoA / 0.683
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.682
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
2c96 ATPPsp operon transcriptional activator / 0.682
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.682
4gp6 ADPMetallophosphoesterase / 0.682
1s1c GNPTransforming protein RhoA / 0.681
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.681
2cls GTPRho-related GTP-binding protein Rho6 / 0.681
3k8y GNPGTPase HRas / 0.681
3tqc ADPPantothenate kinase / 0.681
3vhx GTPADP-ribosylation factor 6 / 0.681
4l9s GDPGTPase HRas / 0.681
4q03 GDPGTPase KRas / 0.681
4ql3 GDPGTPase KRas / 0.681
4rkf GNPRas-related protein Rab-3 / 0.681
5c46 GSPRas-related protein Rab-11A / 0.681
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.680
1rj9 GCPSignal recognition particle receptor FtsY / 0.680
3ref GDPRho family GTPase / 0.680
1b7t ADPMyosin heavy chain, striated muscle / 0.679
1cxz GSPTransforming protein RhoA / 0.679
1l8q ADPChromosomal replication initiator protein DnaA / 0.679
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.679
3cph GDPRas-related protein SEC4 / 0.679
4epx GDPGTPase KRas / 0.679
4lpk GDPGTPase KRas / 0.679
4lv6 GDPGTPase KRas / 0.679
1z2a GDPRas-related protein Rab-23 / 0.678
3k1j ADPATP-dependent protease Lon / 0.678
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.677
4idn GNPAtlastin-1 3.6.5 0.677
1x1r GDPRas-related protein M-Ras / 0.676
1z0f GDPRas-related protein Rab-14 / 0.676
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.676
2rgb GNPGTPase HRas / 0.676
2rge GNPGTPase HRas / 0.676
3oiu GNPGTPase HRas / 0.676
4nyj GNPGTPase HRas / 0.676
1mmg AGSMyosin-2 heavy chain / 0.675
1t91 GTPRas-related protein Rab-7a / 0.675
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.675
3i3s GNPGTPase HRas / 0.675
3k3b ADPKinesin-like protein KIF11 / 0.675
3oiw GNPGTPase HRas / 0.675
3v4f GNPGTPase HRas / 0.675
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.674
1zc4 GNPRas-related protein Ral-A / 0.674
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.674
3rs0 GNPGTPase HRas / 0.674
4dlz GNPGTPase HRas / 0.674
5b2z GNPGTPase HRas / 0.674
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.673
4uj5 GNPRas-related protein Rab-11A / 0.673
1rrg GDPADP-ribosylation factor 1 / 0.672
2iut AGSDNA translocase FtsK / 0.672
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
2x2r ADPKinesin-like protein KIF11 / 0.672
3kz1 GSPTransforming protein RhoA / 0.672
4v02 ATPSite-determining protein / 0.672
5d3q GDPDynamin-1 3.6.5.5 0.672
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.671
2x7e ADPKinesin-like protein KIF11 / 0.671
4mit GTPRho-related protein racC / 0.671
1vg8 GNPRas-related protein Rab-7a / 0.670
2pg2 ADPKinesin-like protein KIF11 / 0.670
3t1t GDPProbable gliding protein mglA / 0.670
4asu ADPATP synthase subunit alpha, mitochondrial / 0.670
4dlt GNPGTPase HRas / 0.670
1svw GTPProbable GTP-binding protein EngB / 0.669
2fna ADPUncharacterized protein / 0.669
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.669
3l8y GNPGTPase HRas / 0.669
4jlo ADPAdenylate kinase / 0.669
2zet GTPRas-related protein Rab-27B / 0.667
4b7b ADPKinesin-like protein KIF11 / 0.667
4hi0 GDPUrease accessory protein UreG / 0.667
4ys0 ADPProtein translocase subunit SecA / 0.667
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.666
1sq5 ADPPantothenate kinase 2.7.1.33 0.666
2qen ADPWalker-Type ATPase / 0.666
4dlv GNPGTPase HRas / 0.666
4l8g GDPGTPase KRas / 0.666
4l9w GNPGTPase HRas / 0.666
3kkq GDPRas-related protein M-Ras / 0.665
3lbi GNPGTPase HRas / 0.665
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.665
3rs4 GNPGTPase HRas / 0.665
3tlx ADPAdenylate kinase 2 / 0.665
4epw GDPGTPase KRas / 0.665
4pjk ADPMyosin-2 heavy chain / 0.665
4tq9 GDPGTPase KRas / 0.665
5ftc ADPTPR domain protein / 0.665
1jx2 ADPMyosin-2 heavy chain / 0.664
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.664
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.664
1wdt GTPElongation factor G (EF-G-2) / 0.664
2ce2 GDPGTPase HRas / 0.664
2fl2 ADPKinesin-like protein KIF11 / 0.664
2rgc GNPGTPase HRas / 0.664
3d8b ADPFidgetin-like protein 1 3.6.4 0.664
3kko GNPRas-related protein M-Ras / 0.664
3rs7 GNPGTPase HRas / 0.664
4cid ANPEH domain-containing protein 2 / 0.664
4jl6 ADPAdenylate kinase / 0.664
4pfp ADPUnconventional myosin-VI / 0.664
4q02 GDPGTPase KRas / 0.664
5aun ADPIron-sulfur cluster carrier protein / 0.664
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.663
3x1w GDPRas-related protein Rap-1b / 0.663
4jky ADPAdenylate kinase / 0.663
4xsg GSPTransforming protein RhoA / 0.663
1wbb ADPDNA mismatch repair protein MutS / 0.662
1z6t ADPApoptotic protease-activating factor 1 / 0.662
2cl6 CAGGTPase HRas / 0.662
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.662
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.662
5bn3 ADPV-type ATP synthase alpha chain / 0.662
5bn3 ADPNEQ263 / 0.662
1f5n GNPGuanylate-binding protein 1 / 0.661
1z0a GDPRas-related protein Rab-2A / 0.661
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.661
3rsl GNPGTPase HRas / 0.661
4a51 ADPKinesin-like protein KIF11 / 0.661
2bc9 GNPGuanylate-binding protein 1 / 0.660
2o8b ADPDNA mismatch repair protein Msh2 / 0.660
3rs5 GNPGTPase HRas / 0.660
4goj GNPADP-ribosylation factor-like protein 3 / 0.660
4h1v GNPDynamin-1-like protein 3.6.5.5 0.660
4js0 GNPCell division control protein 42 homolog / 0.660
4o2l GTPGTP-binding protein Rheb / 0.660
4pk4 ADPUnconventional myosin-VI / 0.660
1k5d GNPGTP-binding nuclear protein Ran / 0.659
3e5h GNPRas-related protein Rab-28 / 0.659
3pit GNPRas-related protein M-Ras / 0.659
1fmw ATPMyosin-2 heavy chain / 0.658
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.658
4nh0 ATPESX secretion system protein EccC / 0.658
4wa7 GDPGTPase KRas / 0.658
2bme GNPRas-related protein Rab-4A / 0.657
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.657
1z2c GNPRho-related GTP-binding protein RhoC / 0.656
3law GNPRas-related protein Rab-7a / 0.656
3lbh GNPGTPase HRas / 0.656
4a28 ADPKinesin-like protein KIF11 / 0.656
4dlw GNPGTPase HRas / 0.656
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.656
1w5t ADPORC1-type DNA replication protein 2 / 0.655
2uyi ADPKinesin-like protein KIF11 / 0.655
4dlx GNPGTPase HRas / 0.655
4dsn GCPGTPase KRas / 0.655
4qbi AP5Adenylate kinase / 0.655
4oi2 ADPProtein clpf-1 / 0.654
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.653
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.653
3tnf GNPRas-related protein Rab-8A / 0.653
4hdq GNPRas-related protein Rap-1b / 0.653
4mkf AP5Adenylate kinase / 0.653
2gm1 ADPKinesin-like protein KIF11 / 0.652
2j5x GSPADP-ribosylation factor 6 / 0.652
3a6p GTPGTP-binding nuclear protein Ran / 0.652
1w5s ADPORC1-type DNA replication protein 2 / 0.651
3ddc GNPGTPase HRas / 0.651
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.651
3l9h ADPKinesin-like protein KIF11 / 0.651
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.650
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
1yra GDPGPN-loop GTPase PAB0955 / 0.650
1zc3 GNPRas-related protein Ral-A / 0.650
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.650
2fe4 GDPRas-related protein Rab-6B / 0.650
5l3s GNPSignal recognition particle receptor FtsY / 0.650