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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
2msc GDP MHC class I alpha chain

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2msc GDPMHC class I alpha chain / 0.893
3lbi GNPGTPase HRas / 0.802
4o25 GTPGTP-binding protein Rheb / 0.799
2ce2 GDPGTPase HRas / 0.788
4dso GSPGTPase KRas / 0.786
3rsl GNPGTPase HRas / 0.784
4dlv GNPGTPase HRas / 0.784
4dlt GNPGTPase HRas / 0.783
2fe4 GDPRas-related protein Rab-6B / 0.782
3l8y GNPGTPase HRas / 0.782
5c46 GSPRas-related protein Rab-11A / 0.781
3mjh GTPRas-related protein Rab-5A / 0.776
4k81 GTPGTPase HRas / 0.775
2rge GNPGTPase HRas / 0.774
3rs0 GNPGTPase HRas / 0.771
3ddc GNPGTPase HRas / 0.770
3oiv GNPGTPase HRas / 0.770
3oiw GNPGTPase HRas / 0.770
3rs4 GNPGTPase HRas / 0.770
3rs5 GNPGTPase HRas / 0.770
1n6l GTPRas-related protein Rab-5A / 0.769
3lbh GNPGTPase HRas / 0.769
4dls GNPGTPase HRas / 0.769
4dlz GNPGTPase HRas / 0.769
2rgc GNPGTPase HRas / 0.768
3k8y GNPGTPase HRas / 0.768
3k9l GNPGTPase HRas / 0.768
4g0n GNPGTPase HRas / 0.768
4hdo GNPRas-related protein Rap-1b / 0.768
4l9w GNPGTPase HRas / 0.766
4q02 GDPGTPase KRas / 0.766
4lpk GDPGTPase KRas / 0.765
1vg8 GNPRas-related protein Rab-7a / 0.760
4lrw GDPGTPase KRas / 0.759
4wa7 GDPGTPase KRas / 0.759
3tgp GNPGTPase HRas / 0.758
3kuc GDPRas-related protein Rap-1A / 0.757
1yzq GNPRas-related protein Rab-6A / 0.756
3x1w GDPRas-related protein Rap-1b / 0.756
3i3s GNPGTPase HRas / 0.755
3oiu GNPGTPase HRas / 0.755
4dlw GNPGTPase HRas / 0.755
3lbn GNPGTPase HRas / 0.754
3rs7 GNPGTPase HRas / 0.754
4dlx GNPGTPase HRas / 0.754
2ffq GSPRas-related protein Rab-6B / 0.753
5b2z GNPGTPase HRas / 0.753
4dsn GCPGTPase KRas / 0.752
4o2r GDPGTP-binding protein Rheb / 0.752
4epw GDPGTPase KRas / 0.751
4ql3 GDPGTPase KRas / 0.751
3tso GNPRas-related protein Rab-25 / 0.750
4nyi GNPGTPase HRas / 0.749
4nyj GNPGTPase HRas / 0.749
3pit GNPRas-related protein M-Ras / 0.747
1tu3 GNPRas-related protein Rab-5A / 0.746
4tq9 GDPGTPase KRas / 0.746
3a58 GNPGTP-binding protein RHO1 / 0.745
4lhw GNPRas-related protein Rab-8A / 0.744
2rgb GNPGTPase HRas / 0.742
4lv6 GDPGTPase KRas / 0.742
3kko GNPRas-related protein M-Ras / 0.741
4l9s GDPGTPase HRas / 0.740
4qxa GTPRas-related protein Rab-9A / 0.739
4xvq GNPGTPase HRas / 0.738
2c5l GTPGTPase HRas / 0.737
3bc1 GNPRas-related protein Rab-27A / 0.737
3e5h GNPRas-related protein Rab-28 / 0.737
3rab GNPRas-related protein Rab-3A / 0.737
4q03 GDPGTPase KRas / 0.737
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.736
1yu9 GNPRas-related protein Rab-4A / 0.735
2dpx GDPGTP-binding protein RAD / 0.735
3v4f GNPGTPase HRas / 0.735
2l0x GDPGTP-binding protein Rheb / 0.733
3x1z GNPRas-related protein Rap-1b / 0.733
4epx GDPGTPase KRas / 0.732
4rkf GNPRas-related protein Rab-3 / 0.731
4dsu GDPGTPase KRas / 0.730
3tnf GNPRas-related protein Rab-8A / 0.728
1zc4 GNPRas-related protein Ral-A / 0.727
4luc GDPGTPase KRas / 0.724
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.723
1z0f GDPRas-related protein Rab-14 / 0.722
4itr GDPCell division control protein 42 homolog / 0.722
4kvg GTPRas-related protein Rap-1A / 0.722
4l8g GDPGTPase KRas / 0.722
2bku GTPGTP-binding nuclear protein Ran / 0.721
1zbd GTPRas-related protein Rab-3A / 0.718
3kud GDPGTPase HRas / 0.718
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.716
1xtr GNPGTP-binding protein Rheb / 0.714
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.711
4hdq GNPRas-related protein Rap-1b / 0.709
1z0d GDPRas-related protein Rab-5C / 0.708
1zc3 GNPRas-related protein Ral-A / 0.708
1lfd GNPGTPase HRas / 0.706
4cym GCPRas-related protein Rab-32 / 0.706
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.706
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.705
3kkq GDPRas-related protein M-Ras / 0.705
2gil GTPRas-related protein Rab-6A / 0.703
4js0 GNPCell division control protein 42 homolog / 0.703
3qbt GNPRas-related protein Rab-8A / 0.702
1ibr GNPGTP-binding nuclear protein Ran / 0.701
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.701
2rgg GNPGTPase HRas / 0.701
4xsg GSPTransforming protein RhoA / 0.701
1x1r GDPRas-related protein M-Ras / 0.698
4lhv GDPRas-related protein Rab-8A / 0.698
2fg5 GNPRas-related protein Rab-31 / 0.697
4d0l GSPRas-related protein Rab-11A / 0.696
4o2l GTPGTP-binding protein Rheb / 0.696
4obe GDPGTPase KRas / 0.696
1z0a GDPRas-related protein Rab-2A / 0.694
5dha GNPGTP-binding nuclear protein Ran / 0.694
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.693
3law GNPRas-related protein Rab-7a / 0.692
5dif GNPGTP-binding nuclear protein Ran / 0.692
1a2b GSPTransforming protein RhoA / 0.691
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.691
1kmq GNPTransforming protein RhoA / 0.691
1oix GDPRas-related protein Rab-11A / 0.691
1z2a GDPRas-related protein Rab-23 / 0.690
3w3z GTPGTP-binding nuclear protein Ran / 0.689
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.688
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.688
1uad GNPRas-related protein Ral-A / 0.686
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.686
1s1c GNPTransforming protein RhoA / 0.685
1z2c GNPRho-related GTP-binding protein RhoC / 0.683
4ylg GDPADP-ribosylation factor 1, putative / 0.683
3ref GDPRho family GTPase / 0.682
1yra GDPGPN-loop GTPase PAB0955 / 0.681
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.681
5d3q GDPDynamin-1 3.6.5.5 0.681
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.680
3nbz GTPGTP-binding nuclear protein Ran / 0.678
1g16 GDPRas-related protein SEC4 / 0.677
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.677
4uj5 GNPRas-related protein Rab-11A / 0.677
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.676
3ea5 GDPGTP-binding nuclear protein Ran / 0.676
1a4r GNHCell division control protein 42 homolog / 0.675
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.674
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.673
2cl6 CAGGTPase HRas / 0.672
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.670
4ncl GDPEukaryotic translation initiation factor 5B / 0.669
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.668
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
5hpy GDPTransforming protein RhoA / 0.668
3cph GDPRas-related protein SEC4 / 0.666
3oes GNPGTPase RhebL1 / 0.666
4dvg GSPRho family GTPase / 0.666
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.665
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.664
3b1x GNPFerrous iron transport protein B / 0.662
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.662
4xvr GNPGTPase HRas / 0.662
5di3 GNPADP-ribosylation factor-like protein 3 / 0.662
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.661
4uj3 GNPRas-related protein Rab-11A / 0.661
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.660
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.660
3r9i ADPSeptum site-determining protein MinD / 0.660
2j5x GSPADP-ribosylation factor 6 / 0.659
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.657
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.657
4y0v GDPADP-ribosylation factor 1, putative / 0.657
1d5c GDPGTPase (Rab6) / 0.656
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.656
4ldj GDPGTPase KRas / 0.655
2gcp GSPRho-related GTP-binding protein RhoC / 0.654
5jlj GNPGTP-binding nuclear protein Ran / 0.653
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.652
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.651
1ow3 GDPTransforming protein RhoA / 0.650
2dft ADPShikimate kinase 2.7.1.71 0.650
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.650