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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
3ieu GDP GTPase Era

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3ieu GDPGTPase Era / 0.990
3ea5 GDPGTP-binding nuclear protein Ran / 0.872
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.869
3vhx GTPADP-ribosylation factor 6 / 0.856
3a6p GTPGTP-binding nuclear protein Ran / 0.834
3tkl GTPRas-related protein Rab-1A / 0.834
4luc GDPGTPase KRas / 0.818
3t1t GDPProbable gliding protein mglA / 0.814
1z0f GDPRas-related protein Rab-14 / 0.809
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.802
4lrw GDPGTPase KRas / 0.801
2j5x GSPADP-ribosylation factor 6 / 0.799
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.796
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.796
5dif GNPGTP-binding nuclear protein Ran / 0.795
3r9x GNPGTPase Era / 0.794
4lpk GDPGTPase KRas / 0.794
4cym GCPRas-related protein Rab-32 / 0.791
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.790
3kz1 GSPTransforming protein RhoA / 0.790
4wa7 GDPGTPase KRas / 0.788
1zbd GTPRas-related protein Rab-3A / 0.786
4hi0 GDPUrease accessory protein UreG / 0.786
4tq9 GDPGTPase KRas / 0.786
1d5c GDPGTPase (Rab6) / 0.785
1z0a GDPRas-related protein Rab-2A / 0.785
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.782
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.781
4epw GDPGTPase KRas / 0.779
3cph GDPRas-related protein SEC4 / 0.778
3x1w GDPRas-related protein Rap-1b / 0.778
2q3f GNPRas-related GTP-binding protein D / 0.777
4epx GDPGTPase KRas / 0.777
1g16 GDPRas-related protein SEC4 / 0.776
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.775
4goj GNPADP-ribosylation factor-like protein 3 / 0.774
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.774
3pcr GTPADP-ribosylation factor 6 / 0.773
3tjz GNPADP-ribosylation factor 1 / 0.773
5dha GNPGTP-binding nuclear protein Ran / 0.773
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.772
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.772
4dsu GDPGTPase KRas / 0.772
4ol0 GTPGTP-binding nuclear protein Ran / 0.769
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.768
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.767
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.767
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.766
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.765
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.762
4kvg GTPRas-related protein Rap-1A / 0.761
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.761
3ref GDPRho family GTPase / 0.760
5jlj GNPGTP-binding nuclear protein Ran / 0.760
1wbb ADPDNA mismatch repair protein MutS / 0.759
4lv6 GDPGTPase KRas / 0.759
1jx2 ADPMyosin-2 heavy chain / 0.758
4pjk ADPMyosin-2 heavy chain / 0.758
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.757
1ibr GNPGTP-binding nuclear protein Ran / 0.757
2zro ADPProtein RecA / 0.757
4g01 GDPRas-related protein RABF2b / 0.757
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.755
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.755
1rrg GDPADP-ribosylation factor 1 / 0.754
2dpx GDPGTP-binding protein RAD / 0.754
4mit GTPRho-related protein racC / 0.753
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.752
3tso GNPRas-related protein Rab-25 / 0.752
5di3 GNPADP-ribosylation factor-like protein 3 / 0.752
1x1r GDPRas-related protein M-Ras / 0.751
4q02 GDPGTPase KRas / 0.750
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.749
2y65 ADPKinesin heavy chain / 0.749
2ce2 GDPGTPase HRas / 0.748
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.747
2zfi ADPKinesin-like protein KIF1A / 0.747
1z2a GDPRas-related protein Rab-23 / 0.746
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.746
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.746
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.746
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.745
2qen ADPWalker-Type ATPase / 0.745
4q03 GDPGTPase KRas / 0.745
2xae ADPKinesin-like protein KIF11 / 0.744
2zrj AGSProtein RecA / 0.744
1m7b GTPRho-related GTP-binding protein RhoE / 0.743
1sq5 ADPPantothenate kinase 2.7.1.33 0.743
4ncl GDPEukaryotic translation initiation factor 5B / 0.743
1oix GDPRas-related protein Rab-11A / 0.742
3kkq GDPRas-related protein M-Ras / 0.742
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.742
4itr GDPCell division control protein 42 homolog / 0.741
1yzq GNPRas-related protein Rab-6A / 0.740
3kud GDPGTPase HRas / 0.740
4fid GDPG protein alpha subunit, putative / 0.739
5aun ADPIron-sulfur cluster carrier protein / 0.739
1vg8 GNPRas-related protein Rab-7a / 0.738
3bbp GTPRas-related protein Rab-6A / 0.738
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.737
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.737
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.737
4obe GDPGTPase KRas / 0.737
2fna ADPUncharacterized protein / 0.736
2xsz ATPRuvB-like 2 3.6.4.12 0.736
3tgp GNPGTPase HRas / 0.735
2fe4 GDPRas-related protein Rab-6B / 0.734
4lhv GDPRas-related protein Rab-8A / 0.734
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.733
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.730
1ow3 GDPTransforming protein RhoA / 0.729
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.729
1z0d GDPRas-related protein Rab-5C / 0.728
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.728
2o8b ADPDNA mismatch repair protein Msh2 / 0.728
4o25 GTPGTP-binding protein Rheb / 0.728
4y0v GDPADP-ribosylation factor 1, putative / 0.728
1gwn GTPRho-related GTP-binding protein RhoE / 0.727
3k9l GNPGTPase HRas / 0.727
4ylg GDPADP-ribosylation factor 1, putative / 0.727
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.726
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.726
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.726
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.726
1yra GDPGPN-loop GTPase PAB0955 / 0.726
1yu9 GNPRas-related protein Rab-4A / 0.726
2gil GTPRas-related protein Rab-6A / 0.726
4jlo ADPAdenylate kinase / 0.726
4ldj GDPGTPase KRas / 0.726
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.725
2fl2 ADPKinesin-like protein KIF11 / 0.725
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.725
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.725
3qbv GDPCell division control protein 42 homolog / 0.725
4a1z ADPKinesin-like protein KIF11 / 0.725
1svw GTPProbable GTP-binding protein EngB / 0.724
1xtr GNPGTP-binding protein Rheb / 0.724
3qbt GNPRas-related protein Rab-8A / 0.723
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.723
4d81 ADPAAA ATPase, central domain protein / 0.722
4dlz GNPGTPase HRas / 0.722
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.721
3r9i ADPSeptum site-determining protein MinD / 0.721
4lhw GNPRas-related protein Rab-8A / 0.721
1uad GNPRas-related protein Ral-A / 0.719
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.719
4cf7 ADPAdenylate kinase / 0.719
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.719
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.719
5cyo GDPSeptin-9 / 0.719
1g6o ADPCag alpha / 0.718
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.718
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.718
4d0l GSPRas-related protein Rab-11A / 0.718
3e5h GNPRas-related protein Rab-28 / 0.717
3kko GNPRas-related protein M-Ras / 0.717
3ea0 ATPATPase, ParA family / 0.716
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.716
4ql3 GDPGTPase KRas / 0.716
2bme GNPRas-related protein Rab-4A / 0.715
3b1x GNPFerrous iron transport protein B / 0.715
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.715
1z2c GNPRho-related GTP-binding protein RhoC / 0.714
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.714
1yrs ADPKinesin-like protein KIF11 / 0.713
4o2r GDPGTP-binding protein Rheb / 0.713
1s1c GNPTransforming protein RhoA / 0.712
1n6l GTPRas-related protein Rab-5A / 0.711
1nly AGSCag alpha / 0.711
4gp6 ADPMetallophosphoesterase / 0.711
4xvq GNPGTPase HRas / 0.711
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.710
1p3j AP5Adenylate kinase / 0.710
4k81 GTPGTPase HRas / 0.710
4o2l GTPGTP-binding protein Rheb / 0.710
5d3q GDPDynamin-1 3.6.5.5 0.710
2ql6 ADPNicotinamide riboside kinase 1 / 0.709
5bn3 ADPV-type ATP synthase alpha chain / 0.709
5bn3 ADPNEQ263 / 0.709
2dr3 ADPUPF0273 protein PH0284 / 0.708
3kuc GDPRas-related protein Rap-1A / 0.708
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.708
4uj3 GNPRas-related protein Rab-11A / 0.708
4xoi GTPTransforming protein RhoA / 0.708
3d8b ADPFidgetin-like protein 1 3.6.4 0.707
3l1c ADPProtein claret segregational / 0.707
3l9h ADPKinesin-like protein KIF11 / 0.707
3q5d GDPAtlastin-1 3.6.5 0.707
2gm1 ADPKinesin-like protein KIF11 / 0.706
1w5s ADPORC1-type DNA replication protein 2 / 0.705
1xmv ADPProtein RecA / 0.705
2zr9 DTPProtein RecA / 0.705
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.705
4asu ADPATP synthase subunit alpha, mitochondrial / 0.705
4b7b ADPKinesin-like protein KIF11 / 0.705
4dlv GNPGTPase HRas / 0.705
4dvg GSPRho family GTPase / 0.705
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.705
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.704
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.704
3tqc ADPPantothenate kinase / 0.704
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.704
1a4r GNHCell division control protein 42 homolog / 0.703
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.703
4a51 ADPKinesin-like protein KIF11 / 0.703
4jld ADPAdenylate kinase / 0.703
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.703
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.703
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.702
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.702
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.701
4jl6 ADPAdenylate kinase / 0.701
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.700
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.700
4hdq GNPRas-related protein Rap-1b / 0.700
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.699
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.699
3eg5 GNPCell division control protein 42 homolog / 0.699
4dzz ADPPlasmid partitioning protein ParF / 0.699
2ffq GSPRas-related protein Rab-6B / 0.698
3a58 GNPGTP-binding protein RHO1 / 0.698
3rab GNPRas-related protein Rab-3A / 0.698
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.697
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.697
1l8q ADPChromosomal replication initiator protein DnaA / 0.696
2gcp GSPRho-related GTP-binding protein RhoC / 0.696
4xsg GSPTransforming protein RhoA / 0.696
3tnf GNPRas-related protein Rab-8A / 0.695
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.694
1kmq GNPTransforming protein RhoA / 0.693
1w5t ADPORC1-type DNA replication protein 2 / 0.693
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.693
4dsn GCPGTPase KRas / 0.693
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.692
1am4 GNPCell division control protein 42 homolog / 0.691
4js0 GNPCell division control protein 42 homolog / 0.691
1zc4 GNPRas-related protein Ral-A / 0.690
3ftq GNPSeptin-2 / 0.690
2l0x GDPGTP-binding protein Rheb / 0.689
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.689
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.689
4dlx GNPGTPase HRas / 0.689
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.689
2pg2 ADPKinesin-like protein KIF11 / 0.688
2zts ADPUncharacterized protein / 0.688
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.687
2x2r ADPKinesin-like protein KIF11 / 0.687
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.687
4pjj ADPUnconventional myosin-VI / 0.687
1z6t ADPApoptotic protease-activating factor 1 / 0.685
1zc3 GNPRas-related protein Ral-A / 0.685
4dlt GNPGTPase HRas / 0.685
1lfd GNPGTPase HRas / 0.684
1svm ATPLarge T antigen 3.6.4 0.684
2g1q ADPKinesin-like protein KIF11 / 0.684
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.684
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.684
2uyi ADPKinesin-like protein KIF11 / 0.684
2whx ADPGenome polyprotein 3.4.21.91 0.684
3ddc GNPGTPase HRas / 0.684
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.684
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.683
4z54 GDPNeuronal-specific septin-3 / 0.683
3lbh GNPGTPase HRas / 0.681
4yqf GDPSeptin-9 / 0.681
3oiv GNPGTPase HRas / 0.679
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.678
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.678
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.677
1e4y AP5Adenylate kinase / 0.676
2bbw GP5Adenylate kinase 4, mitochondrial / 0.676
1b7t ADPMyosin heavy chain, striated muscle / 0.675
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.675
5c46 GSPRas-related protein Rab-11A / 0.675
3dm5 GDPSignal recognition particle 54 kDa protein / 0.674
3i3s GNPGTPase HRas / 0.674
4a28 ADPKinesin-like protein KIF11 / 0.674
2rgc GNPGTPase HRas / 0.673
2vf7 ADPUvrABC system protein A / 0.673
3tlx ADPAdenylate kinase 2 / 0.673
4xvr GNPGTPase HRas / 0.673
1n6m ADPProtein claret segregational / 0.671
4h1v GNPDynamin-1-like protein 3.6.5.5 0.670
2rgb GNPGTPase HRas / 0.669
2rge GNPGTPase HRas / 0.669
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.669
1wa5 GTPGTP-binding nuclear protein Ran / 0.668
2x7e ADPKinesin-like protein KIF11 / 0.667
4uj5 GNPRas-related protein Rab-11A / 0.667
3c41 ANPAmino acid ABC transporter / 0.666
4pk4 ADPUnconventional myosin-VI / 0.666
5ftf ADPTPR domain protein / 0.666
1wdt GTPElongation factor G (EF-G-2) / 0.665
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
3oes GNPGTPase RhebL1 / 0.665
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.664
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.663
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.663
1p9w ANPType II secretion system protein E / 0.662
2c9o ADPRuvB-like 1 3.6.4.12 0.662
2zet GTPRas-related protein Rab-27B / 0.662
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.661
1eyn 2ANUDP-N-acetylglucosamine 1-carboxyvinyltransferase / 0.660
1svl ADPLarge T antigen 3.6.4 0.660
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.660
2xf3 J01Uncharacterized protein / 0.660
2xvv 9DNSerum albumin / 0.660
3cz0 9ODPheromone-binding protein ASP1 / 0.660
3fo7 IMNPhospholipase A2 VRV-PL-VIIIa / 0.660
3nfa CBJGag-Pol polyprotein / 0.660
3ngq 1PSCCR4-NOT transcription complex subunit 6-like 3.1.13.4 0.660
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.660
4c1f X8ZMetallo-beta-lactamase type 2 / 0.660
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.660
4dsb A8SAbscisic acid receptor PYL3 / 0.660
4kla CHDFerrochelatase, mitochondrial 4.99.1.1 0.660
5dby DIFSerum albumin / 0.660
5dby NPSSerum albumin / 0.660
5jqb IBPEnvelope glycoprotein / 0.660
2qd3 CHDFerrochelatase, mitochondrial 4.99.1.1 0.659
4pfp ADPUnconventional myosin-VI / 0.659
1k5d GNPGTP-binding nuclear protein Ran / 0.656
2r9v ATPATP synthase subunit alpha / 0.655
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.655
4hse ADPChaperone protein ClpB / 0.655
4qxa GTPRas-related protein Rab-9A / 0.654
2bku GTPGTP-binding nuclear protein Ran / 0.652
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.652
3mjh GTPRas-related protein Rab-5A / 0.651
1sxj ADPReplication factor C subunit 5 / 0.650
3dzd ADPTranscriptional regulator (NtrC family) / 0.650
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.650