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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
4fid GDP G protein alpha subunit, putative

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4fid GDPG protein alpha subunit, putative / 1.073
1wa5 GTPGTP-binding nuclear protein Ran / 0.769
3w3z GTPGTP-binding nuclear protein Ran / 0.762
2j5x GSPADP-ribosylation factor 6 / 0.741
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.740
3ieu GDPGTPase Era / 0.739
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.737
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.736
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.734
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.734
3wyf GTPGTP-binding nuclear protein / 0.733
3ea5 GDPGTP-binding nuclear protein Ran / 0.732
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.730
2zet GTPRas-related protein Rab-27B / 0.730
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.729
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.728
1z0d GDPRas-related protein Rab-5C / 0.722
3vhx GTPADP-ribosylation factor 6 / 0.722
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.720
4g0n GNPGTPase HRas / 0.719
1d5c GDPGTPase (Rab6) / 0.718
1ibr GNPGTP-binding nuclear protein Ran / 0.718
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.716
2bku GTPGTP-binding nuclear protein Ran / 0.715
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.714
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.714
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.712
3tjz GNPADP-ribosylation factor 1 / 0.709
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.708
4g01 GDPRas-related protein RABF2b / 0.703
3a6p GTPGTP-binding nuclear protein Ran / 0.701
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.700
5jlj GNPGTP-binding nuclear protein Ran / 0.700
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.698
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.696
5dif GNPGTP-binding nuclear protein Ran / 0.694
3cph GDPRas-related protein SEC4 / 0.690
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.690
5dha GNPGTP-binding nuclear protein Ran / 0.690
3b1x GNPFerrous iron transport protein B / 0.689
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.688
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.688
2xto GDPGTPase IMAP family member 2 / 0.687
1t91 GTPRas-related protein Rab-7a / 0.686
1z2a GDPRas-related protein Rab-23 / 0.686
1yra GDPGPN-loop GTPase PAB0955 / 0.685
3t1t GDPProbable gliding protein mglA / 0.681
1zbd GTPRas-related protein Rab-3A / 0.679
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.679
1xtr GNPGTP-binding protein Rheb / 0.678
4goj GNPADP-ribosylation factor-like protein 3 / 0.677
2j7p GNPSignal recognition particle protein / 0.673
2j7p GNPSignal recognition particle receptor FtsY / 0.673
2x19 GTPGTP-binding nuclear protein GSP1/CNR1 / 0.673
4jky ADPAdenylate kinase / 0.671
4ol0 GTPGTP-binding nuclear protein Ran / 0.670
3bbp GTPRas-related protein Rab-6A / 0.669
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.668
3qi2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
2q3f GNPRas-related GTP-binding protein D / 0.667
4qxa GTPRas-related protein Rab-9A / 0.667
4y0v GDPADP-ribosylation factor 1, putative / 0.667
1rrg GDPADP-ribosylation factor 1 / 0.666
3pcr GTPADP-ribosylation factor 6 / 0.665
4ncl GDPEukaryotic translation initiation factor 5B / 0.665
4ylg GDPADP-ribosylation factor 1, putative / 0.665
3nbz GTPGTP-binding nuclear protein Ran / 0.663
3r9x GNPGTPase Era / 0.661
1rj9 GCPSignal recognition particle receptor FtsY / 0.660
3kud GDPGTPase HRas / 0.660
3rab GNPRas-related protein Rab-3A / 0.660
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.659
1oix GDPRas-related protein Rab-11A / 0.658
3k9l GNPGTPase HRas / 0.658
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.658
5l3s GNPSignal recognition particle receptor FtsY / 0.658
2fe4 GDPRas-related protein Rab-6B / 0.656
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.656
3kuc GDPRas-related protein Rap-1A / 0.656
1z0a GDPRas-related protein Rab-2A / 0.655
4dlz GNPGTPase HRas / 0.654
4jlo ADPAdenylate kinase / 0.654
4ql3 GDPGTPase KRas / 0.654
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.653
1zc3 GNPRas-related protein Ral-A / 0.653
2zr9 DTPProtein RecA / 0.653
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.653
1jx2 ADPMyosin-2 heavy chain / 0.652
4jld ADPAdenylate kinase / 0.652
4l9s GDPGTPase HRas / 0.652
4o25 GTPGTP-binding protein Rheb / 0.652
3thy ADPDNA mismatch repair protein Msh2 / 0.651
4lhv GDPRas-related protein Rab-8A / 0.651
1vg8 GNPRas-related protein Rab-7a / 0.650
5bn3 ADPV-type ATP synthase alpha chain / 0.650
5bn3 ADPNEQ263 / 0.650