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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
1a4r GNH Cell division control protein 42 homolog

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1a4r GNHCell division control protein 42 homolog / 0.912
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.860
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.860
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.855
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.853
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.845
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.842
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.836
1ow3 GDPTransforming protein RhoA / 0.835
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.834
1s1c GNPTransforming protein RhoA / 0.831
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.831
3a58 GNPGTP-binding protein RHO1 / 0.829
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.827
4itr GDPCell division control protein 42 homolog / 0.827
4js0 GNPCell division control protein 42 homolog / 0.827
4lhw GNPRas-related protein Rab-8A / 0.827
4xsg GSPTransforming protein RhoA / 0.827
1g17 GNPRas-related protein SEC4 / 0.824
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.823
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.821
1d5c GDPGTPase (Rab6) / 0.819
4lhv GDPRas-related protein Rab-8A / 0.819
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.814
4g0n GNPGTPase HRas / 0.813
2gil GTPRas-related protein Rab-6A / 0.811
4kvg GTPRas-related protein Rap-1A / 0.809
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.808
3ref GDPRho family GTPase / 0.804
3x1w GDPRas-related protein Rap-1b / 0.804
3tnf GNPRas-related protein Rab-8A / 0.803
3mjh GTPRas-related protein Rab-5A / 0.802
1yu9 GNPRas-related protein Rab-4A / 0.800
1tu3 GNPRas-related protein Rab-5A / 0.799
3kud GDPGTPase HRas / 0.798
4lv6 GDPGTPase KRas / 0.798
4dxa GSPRas-related protein Rap-1b / 0.797
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.796
1zbd GTPRas-related protein Rab-3A / 0.796
3rab GNPRas-related protein Rab-3A / 0.796
2ffq GSPRas-related protein Rab-6B / 0.795
4mit GTPRho-related protein racC / 0.795
4hdo GNPRas-related protein Rap-1b / 0.793
4nyj GNPGTPase HRas / 0.793
4xoi GTPTransforming protein RhoA / 0.793
1g16 GDPRas-related protein SEC4 / 0.792
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.791
2gcp GSPRho-related GTP-binding protein RhoC / 0.789
1a2b GSPTransforming protein RhoA / 0.788
1kmq GNPTransforming protein RhoA / 0.788
2bme GNPRas-related protein Rab-4A / 0.788
2fe4 GDPRas-related protein Rab-6B / 0.788
3x1z GNPRas-related protein Rap-1b / 0.788
1z0f GDPRas-related protein Rab-14 / 0.787
1z0a GDPRas-related protein Rab-2A / 0.786
3rs5 GNPGTPase HRas / 0.785
4dsu GDPGTPase KRas / 0.785
4q03 GDPGTPase KRas / 0.784
1n6l GTPRas-related protein Rab-5A / 0.783
2ce2 GDPGTPase HRas / 0.782
1z0d GDPRas-related protein Rab-5C / 0.781
3k8y GNPGTPase HRas / 0.781
4ldj GDPGTPase KRas / 0.781
1m7b GTPRho-related GTP-binding protein RhoE / 0.780
3lbi GNPGTPase HRas / 0.780
3oiw GNPGTPase HRas / 0.779
4q02 GDPGTPase KRas / 0.779
4epx GDPGTPase KRas / 0.778
3qbt GNPRas-related protein Rab-8A / 0.777
4epw GDPGTPase KRas / 0.777
1zc4 GNPRas-related protein Ral-A / 0.776
3eg5 GNPCell division control protein 42 homolog / 0.776
4wa7 GDPGTPase KRas / 0.775
3tso GNPRas-related protein Rab-25 / 0.774
1xtr GNPGTP-binding protein Rheb / 0.773
4dvg GSPRho family GTPase / 0.773
4rkf GNPRas-related protein Rab-3 / 0.773
1cxz GSPTransforming protein RhoA / 0.772
4xvr GNPGTPase HRas / 0.772
4l9s GDPGTPase HRas / 0.771
1gwn GTPRho-related GTP-binding protein RhoE / 0.770
3kko GNPRas-related protein M-Ras / 0.770
3rs4 GNPGTPase HRas / 0.769
3rs7 GNPGTPase HRas / 0.769
4l9w GNPGTPase HRas / 0.769
2cls GTPRho-related GTP-binding protein Rho6 / 0.768
3tgp GNPGTPase HRas / 0.768
4o2l GTPGTP-binding protein Rheb / 0.768
2rgb GNPGTPase HRas / 0.767
3k9l GNPGTPase HRas / 0.767
2rge GNPGTPase HRas / 0.766
4dso GSPGTPase KRas / 0.766
1lfd GNPGTPase HRas / 0.765
3i3s GNPGTPase HRas / 0.765
3oiu GNPGTPase HRas / 0.765
4dlt GNPGTPase HRas / 0.765
4dlv GNPGTPase HRas / 0.765
3rs0 GNPGTPase HRas / 0.764
3v4f GNPGTPase HRas / 0.764
4dlw GNPGTPase HRas / 0.764
5di3 GNPADP-ribosylation factor-like protein 3 / 0.764
1ibr GNPGTP-binding nuclear protein Ran / 0.763
2rgc GNPGTPase HRas / 0.763
2rgg GNPGTPase HRas / 0.763
3l8y GNPGTPase HRas / 0.763
3rsl GNPGTPase HRas / 0.763
1t91 GTPRas-related protein Rab-7a / 0.761
1zc3 GNPRas-related protein Ral-A / 0.760
3kuc GDPRas-related protein Rap-1A / 0.759
4lpk GDPGTPase KRas / 0.758
4ql3 GDPGTPase KRas / 0.758
4dls GNPGTPase HRas / 0.757
4qxa GTPRas-related protein Rab-9A / 0.757
3w3z GTPGTP-binding nuclear protein Ran / 0.756
4tq9 GDPGTPase KRas / 0.755
5dha GNPGTP-binding nuclear protein Ran / 0.755
3tkl GTPRas-related protein Rab-1A / 0.754
1yzq GNPRas-related protein Rab-6A / 0.753
3e5h GNPRas-related protein Rab-28 / 0.753
4cym GCPRas-related protein Rab-32 / 0.753
5c46 GSPRas-related protein Rab-11A / 0.753
4k81 GTPGTPase HRas / 0.752
5jlj GNPGTP-binding nuclear protein Ran / 0.752
3ddc GNPGTPase HRas / 0.751
3cph GDPRas-related protein SEC4 / 0.750
2bku GTPGTP-binding nuclear protein Ran / 0.749
1uad GNPRas-related protein Ral-A / 0.747
2j5x GSPADP-ribosylation factor 6 / 0.747
3oiv GNPGTPase HRas / 0.747
5b2z GNPGTPase HRas / 0.747
1xts GTPGTP-binding protein Rheb / 0.746
2c5l GTPGTPase HRas / 0.745
4o2r GDPGTP-binding protein Rheb / 0.742
3bc1 GNPRas-related protein Rab-27A / 0.741
3pit GNPRas-related protein M-Ras / 0.740
4nyi GNPGTPase HRas / 0.740
2fg5 GNPRas-related protein Rab-31 / 0.738
1x1r GDPRas-related protein M-Ras / 0.737
3b1x GNPFerrous iron transport protein B / 0.736
1z2a GDPRas-related protein Rab-23 / 0.735
1z2c GNPRho-related GTP-binding protein RhoC / 0.735
4y0v GDPADP-ribosylation factor 1, putative / 0.734
4ylg GDPADP-ribosylation factor 1, putative / 0.734
3lbh GNPGTPase HRas / 0.732
3lbn GNPGTPase HRas / 0.732
4lrw GDPGTPase KRas / 0.732
4o25 GTPGTP-binding protein Rheb / 0.732
3vhx GTPADP-ribosylation factor 6 / 0.731
4obe GDPGTPase KRas / 0.730
5dif GNPGTP-binding nuclear protein Ran / 0.728
4d0l GSPRas-related protein Rab-11A / 0.726
4uj3 GNPRas-related protein Rab-11A / 0.726
4uj5 GNPRas-related protein Rab-11A / 0.726
5hpy GDPTransforming protein RhoA / 0.726
3oes GNPGTPase RhebL1 / 0.725
4l8g GDPGTPase KRas / 0.725
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.724
2dpx GDPGTP-binding protein RAD / 0.723
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.723
3kz1 GSPTransforming protein RhoA / 0.723
1ky2 GNPGTP-binding protein YPT7 / 0.722
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.721
1wa5 GTPGTP-binding nuclear protein Ran / 0.719
2fna ADPUncharacterized protein / 0.719
1yra GDPGPN-loop GTPase PAB0955 / 0.718
4goj GNPADP-ribosylation factor-like protein 3 / 0.718
4hdq GNPRas-related protein Rap-1b / 0.717
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.716
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.713
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.713
3ea5 GDPGTP-binding nuclear protein Ran / 0.712
3tqc ADPPantothenate kinase / 0.712
4xvq GNPGTPase HRas / 0.712
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.710
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.709
3kkq GDPRas-related protein M-Ras / 0.709
1oix GDPRas-related protein Rab-11A / 0.707
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.706
4luc GDPGTPase KRas / 0.706
4g01 GDPRas-related protein RABF2b / 0.705
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.704
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.704
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.703
3ieu GDPGTPase Era / 0.703
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.703
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.701
3r9i ADPSeptum site-determining protein MinD / 0.700
1rrg GDPADP-ribosylation factor 1 / 0.699
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.698
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.696
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.696
2y65 ADPKinesin heavy chain / 0.696
4dsn GCPGTPase KRas / 0.696
4ihq ADPConserved Archaeal protein / 0.696
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.695
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.694
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.694
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.693
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.692
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.692
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.692
1sq5 ADPPantothenate kinase 2.7.1.33 0.691
2l0x GDPGTP-binding protein Rheb / 0.691
4ncl GDPEukaryotic translation initiation factor 5B / 0.690
1vg8 GNPRas-related protein Rab-7a / 0.688
4hse ADPChaperone protein ClpB / 0.688
3wyf GTPGTP-binding nuclear protein / 0.687
4v02 ATPSite-determining protein / 0.687
4pfp ADPUnconventional myosin-VI / 0.686
5aun ADPIron-sulfur cluster carrier protein / 0.686
1z6t ADPApoptotic protease-activating factor 1 / 0.685
4pjk ADPMyosin-2 heavy chain / 0.684
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.683
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.683
4pjj ADPUnconventional myosin-VI / 0.683
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.682
1fmw ATPMyosin-2 heavy chain / 0.681
3m0e ATPTranscriptional regulator (NtrC family) / 0.681
4cf7 ADPAdenylate kinase / 0.681
1fnn ADPORC1-type DNA replication protein / 0.679
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.679
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
3t1t GDPProbable gliding protein mglA / 0.679
3zia ATPATP synthase subunit alpha, mitochondrial / 0.679
4db1 ANPMyosin-7 / 0.679
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.678
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.678
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.678
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.677
1sdm ADPKinesin heavy chain-like protein / 0.677
2uyi ADPKinesin-like protein KIF11 / 0.677
2zfi ADPKinesin-like protein KIF1A / 0.677
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.676
1w5t ANPORC1-type DNA replication protein 2 / 0.676
2gm1 ADPKinesin-like protein KIF11 / 0.675
2msc GDPMHC class I alpha chain / 0.675
1yhn GTPRas-related protein Rab-7a / 0.674
2x2r ADPKinesin-like protein KIF11 / 0.674
3l9h ADPKinesin-like protein KIF11 / 0.674
5d3q GDPDynamin-1 3.6.5.5 0.673
2xae ADPKinesin-like protein KIF11 / 0.672
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.672
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.671
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.671
4b7b ADPKinesin-like protein KIF11 / 0.671
4x8l AP5Adenylate kinase / 0.671
5bn3 ADPV-type ATP synthase alpha chain / 0.671
5bn3 ADPNEQ263 / 0.671
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.670
1wbb ADPDNA mismatch repair protein MutS / 0.670
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.670
3qbv GDPCell division control protein 42 homolog / 0.670
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.669
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.669
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.669
2q2y ADPKinesin-like protein KIF11 / 0.669
2zet GTPRas-related protein Rab-27B / 0.669
1jx2 ADPMyosin-2 heavy chain / 0.668
1l8q ADPChromosomal replication initiator protein DnaA / 0.668
2bc9 GNPGuanylate-binding protein 1 / 0.668
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.668
5bn4 ANPV-type ATP synthase alpha chain / 0.668
4o3m ADPBloom syndrome protein 3.6.4.12 0.667
5ftc ADPTPR domain protein / 0.667
1yrs ADPKinesin-like protein KIF11 / 0.666
2qen ADPWalker-Type ATPase / 0.666
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.666
3zfd ANPChromosome-associated kinesin KIF4 / 0.666
4a28 ADPKinesin-like protein KIF11 / 0.666
4jjz ADPFormate--tetrahydrofolate ligase / 0.666
1ank ANPAdenylate kinase / 0.665
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
2cl6 CAGGTPase HRas / 0.665
4gp6 ADPMetallophosphoesterase / 0.665
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.665
4ol0 GTPGTP-binding nuclear protein Ran / 0.664
5fl3 ADPPili retraction protein PilT / 0.664
1b7t ADPMyosin heavy chain, striated muscle / 0.663
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.663
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.663
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.663
2c96 ATPPsp operon transcriptional activator / 0.662
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.662
2pg2 ADPKinesin-like protein KIF11 / 0.662
3pcr GTPADP-ribosylation factor 6 / 0.662
4asu ADPATP synthase subunit alpha, mitochondrial / 0.662
1g6o ADPCag alpha / 0.661
1mma ADPMyosin-2 heavy chain / 0.661
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.661
4mkf AP5Adenylate kinase / 0.661
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.660
2xsz ATPRuvB-like 2 3.6.4.12 0.660
4iok ADPFormate--tetrahydrofolate ligase / 0.660
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.660
5k5z ANPUncharacterized protein / 0.660
2ql6 ADPNicotinamide riboside kinase 1 / 0.659
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.659
2x7e ADPKinesin-like protein KIF11 / 0.658
3tjz GNPADP-ribosylation factor 1 / 0.658
4dlx GNPGTPase HRas / 0.658
4x8o AP5Adenylate kinase / 0.658
2ad5 ADPCTP synthase / 0.657
2zts ADPUncharacterized protein / 0.657
3bbp GTPRas-related protein Rab-6A / 0.657
4z54 GDPNeuronal-specific septin-3 / 0.657
1am4 GNPCell division control protein 42 homolog / 0.656
2bbw GP5Adenylate kinase 4, mitochondrial / 0.656
2fl2 ADPKinesin-like protein KIF11 / 0.656
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.656
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
2zr9 DTPProtein RecA / 0.656
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.655
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.655
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
3k1j ADPATP-dependent protease Lon / 0.655
5cyo GDPSeptin-9 / 0.655
4a1z ADPKinesin-like protein KIF11 / 0.654
4c2u ANPDNA helicase / 0.654
4hi0 GDPUrease accessory protein UreG / 0.654
4pk4 ADPUnconventional myosin-VI / 0.654
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.654
1ii6 ADPKinesin-like protein KIF11 / 0.653
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.653
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.653
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
2hld ANPATP synthase subunit alpha, mitochondrial / 0.652
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.650
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
3myk ANPMyosin-2 heavy chain / 0.650
4d81 ADPAAA ATPase, central domain protein / 0.650