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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
1yhn GTP Ras-related protein Rab-7a

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1yhn GTPRas-related protein Rab-7a / 1.163
3tnf GNPRas-related protein Rab-8A / 0.868
1vg8 GNPRas-related protein Rab-7a / 0.865
3mjh GTPRas-related protein Rab-5A / 0.861
3e5h GNPRas-related protein Rab-28 / 0.841
1n6l GTPRas-related protein Rab-5A / 0.824
1yzq GNPRas-related protein Rab-6A / 0.812
4qxa GTPRas-related protein Rab-9A / 0.807
1g17 GNPRas-related protein SEC4 / 0.806
2gil GTPRas-related protein Rab-6A / 0.797
1zc4 GNPRas-related protein Ral-A / 0.789
3tso GNPRas-related protein Rab-25 / 0.781
4dso GSPGTPase KRas / 0.779
4kvg GTPRas-related protein Rap-1A / 0.775
1z0d GDPRas-related protein Rab-5C / 0.771
3bc1 GNPRas-related protein Rab-27A / 0.771
3rab GNPRas-related protein Rab-3A / 0.771
3bbp GTPRas-related protein Rab-6A / 0.769
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.769
4nyi GNPGTPase HRas / 0.767
1xtr GNPGTP-binding protein Rheb / 0.765
1zc3 GNPRas-related protein Ral-A / 0.764
3tkl GTPRas-related protein Rab-1A / 0.763
4nyj GNPGTPase HRas / 0.760
3w3z GTPGTP-binding nuclear protein Ran / 0.757
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.756
3k8y GNPGTPase HRas / 0.753
5di3 GNPADP-ribosylation factor-like protein 3 / 0.747
3law GNPRas-related protein Rab-7a / 0.744
3lbh GNPGTPase HRas / 0.740
3rsl GNPGTPase HRas / 0.740
2rgg GNPGTPase HRas / 0.737
4dls GNPGTPase HRas / 0.735
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.734
3rs0 GNPGTPase HRas / 0.734
2rge GNPGTPase HRas / 0.732
1wa5 GTPGTP-binding nuclear protein Ran / 0.731
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.731
3a58 GNPGTP-binding protein RHO1 / 0.730
3oiw GNPGTPase HRas / 0.730
3oiv GNPGTPase HRas / 0.729
4lrw GDPGTPase KRas / 0.729
2fg5 GNPRas-related protein Rab-31 / 0.726
1lfd GNPGTPase HRas / 0.725
2fe4 GDPRas-related protein Rab-6B / 0.725
4dlt GNPGTPase HRas / 0.725
3ddc GNPGTPase HRas / 0.724
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.723
5c46 GSPRas-related protein Rab-11A / 0.723
2c5l GTPGTPase HRas / 0.721
3lbi GNPGTPase HRas / 0.720
4dlv GNPGTPase HRas / 0.720
3rs7 GNPGTPase HRas / 0.719
3k9l GNPGTPase HRas / 0.718
2bku GTPGTP-binding nuclear protein Ran / 0.717
4uj3 GNPRas-related protein Rab-11A / 0.716
2rgc GNPGTPase HRas / 0.715
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.714
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.713
1zbd GTPRas-related protein Rab-3A / 0.713
2ffq GSPRas-related protein Rab-6B / 0.713
3cph GDPRas-related protein SEC4 / 0.713
3lbn GNPGTPase HRas / 0.710
4dxa GSPRas-related protein Rap-1b / 0.708
3qbt GNPRas-related protein Rab-8A / 0.707
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.706
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.704
1yu9 GNPRas-related protein Rab-4A / 0.703
4ol0 GTPGTP-binding nuclear protein Ran / 0.703
4dlx GNPGTPase HRas / 0.702
4uj5 GNPRas-related protein Rab-11A / 0.702
3wyf GTPGTP-binding nuclear protein / 0.701
2rgb GNPGTPase HRas / 0.700
4xvr GNPGTPase HRas / 0.700
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.699
4epw GDPGTPase KRas / 0.697
4o2l GTPGTP-binding protein Rheb / 0.696
4k81 GTPGTPase HRas / 0.694
3nbz GTPGTP-binding nuclear protein Ran / 0.693
4xsg GSPTransforming protein RhoA / 0.693
4dsu GDPGTPase KRas / 0.692
3r9x GNPGTPase Era / 0.691
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.690
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.690
4hdq GNPRas-related protein Rap-1b / 0.690
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.689
3vhx GTPADP-ribosylation factor 6 / 0.688
1uad GNPRas-related protein Ral-A / 0.686
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.683
4lhw GNPRas-related protein Rab-8A / 0.683
4goj GNPADP-ribosylation factor-like protein 3 / 0.682
4dlz GNPGTPase HRas / 0.680
4wa7 GDPGTPase KRas / 0.678
3kz1 GSPTransforming protein RhoA / 0.676
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.676
5b2z GNPGTPase HRas / 0.676
1a4r GNHCell division control protein 42 homolog / 0.674
1yra GDPGPN-loop GTPase PAB0955 / 0.674
2zet GTPRas-related protein Rab-27B / 0.674
4dsn GCPGTPase KRas / 0.673
1z0a GDPRas-related protein Rab-2A / 0.672
1xts GTPGTP-binding protein Rheb / 0.671
3t1t GDPProbable gliding protein mglA / 0.671
1ky2 GNPGTP-binding protein YPT7 / 0.670
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.668
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.665
3a6p GTPGTP-binding nuclear protein Ran / 0.665
3i3s GNPGTPase HRas / 0.664
1tu3 GNPRas-related protein Rab-5A / 0.663
2cl6 CAGGTPase HRas / 0.661
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.660
2x19 GTPGTP-binding nuclear protein GSP1/CNR1 / 0.660
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.660
4cym GCPRas-related protein Rab-32 / 0.659
4o2r GDPGTP-binding protein Rheb / 0.654
4v02 ATPSite-determining protein / 0.653
3tgp GNPGTPase HRas / 0.652
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.652
3kuc GDPRas-related protein Rap-1A / 0.651
1k5d GNPGTP-binding nuclear protein Ran / 0.650
4g0n GNPGTPase HRas / 0.650