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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
2zet GTP Ras-related protein Rab-27B

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2zet GTPRas-related protein Rab-27B / 1.248
1zbd GTPRas-related protein Rab-3A / 0.950
3tkl GTPRas-related protein Rab-1A / 0.878
5c46 GSPRas-related protein Rab-11A / 0.871
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.866
1xts GTPGTP-binding protein Rheb / 0.849
3bbp GTPRas-related protein Rab-6A / 0.842
3tso GNPRas-related protein Rab-25 / 0.837
4kvg GTPRas-related protein Rap-1A / 0.836
1ibr GNPGTP-binding nuclear protein Ran / 0.832
3e5h GNPRas-related protein Rab-28 / 0.828
4cym GCPRas-related protein Rab-32 / 0.828
3a58 GNPGTP-binding protein RHO1 / 0.827
4k81 GTPGTPase HRas / 0.819
4g0n GNPGTPase HRas / 0.817
1z2c GNPRho-related GTP-binding protein RhoC / 0.814
1tu3 GNPRas-related protein Rab-5A / 0.813
3law GNPRas-related protein Rab-7a / 0.811
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.809
3w3z GTPGTP-binding nuclear protein Ran / 0.809
2fg5 GNPRas-related protein Rab-31 / 0.806
3lbi GNPGTPase HRas / 0.806
1zc4 GNPRas-related protein Ral-A / 0.801
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.800
1t91 GTPRas-related protein Rab-7a / 0.799
1yzq GNPRas-related protein Rab-6A / 0.799
3r9x GNPGTPase Era / 0.799
4mit GTPRho-related protein racC / 0.799
1g17 GNPRas-related protein SEC4 / 0.798
3tnf GNPRas-related protein Rab-8A / 0.795
1vg8 GNPRas-related protein Rab-7a / 0.794
1xtr GNPGTP-binding protein Rheb / 0.793
1gwn GTPRho-related GTP-binding protein RhoE / 0.791
4o25 GTPGTP-binding protein Rheb / 0.791
3lbn GNPGTPase HRas / 0.790
3kz1 GSPTransforming protein RhoA / 0.789
3mjh GTPRas-related protein Rab-5A / 0.789
4hdo GNPRas-related protein Rap-1b / 0.789
5dha GNPGTP-binding nuclear protein Ran / 0.789
4lhw GNPRas-related protein Rab-8A / 0.788
4dvg GSPRho family GTPase / 0.786
4uj5 GNPRas-related protein Rab-11A / 0.786
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.785
4dlt GNPGTPase HRas / 0.783
1k5d GNPGTP-binding nuclear protein Ran / 0.781
3bc1 GNPRas-related protein Rab-27A / 0.781
3eg5 GNPCell division control protein 42 homolog / 0.781
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.780
3k8y GNPGTPase HRas / 0.780
5dif GNPGTP-binding nuclear protein Ran / 0.780
3qbt GNPRas-related protein Rab-8A / 0.778
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.776
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.776
4xoi GTPTransforming protein RhoA / 0.776
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.775
2c5l GTPGTPase HRas / 0.775
3rsl GNPGTPase HRas / 0.774
5b2z GNPGTPase HRas / 0.774
2rgb GNPGTPase HRas / 0.772
4qxa GTPRas-related protein Rab-9A / 0.771
5jlj GNPGTP-binding nuclear protein Ran / 0.771
2ffq GSPRas-related protein Rab-6B / 0.770
4dlz GNPGTPase HRas / 0.770
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.769
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.768
3a6p GTPGTP-binding nuclear protein Ran / 0.768
3kko GNPRas-related protein M-Ras / 0.767
3x1z GNPRas-related protein Rap-1b / 0.767
4dso GSPGTPase KRas / 0.767
1a2b GSPTransforming protein RhoA / 0.766
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.766
3b1x GNPFerrous iron transport protein B / 0.766
1kmq GNPTransforming protein RhoA / 0.765
3kud GDPGTPase HRas / 0.764
3oiv GNPGTPase HRas / 0.764
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.764
4nyi GNPGTPase HRas / 0.764
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.763
1n6l GTPRas-related protein Rab-5A / 0.762
3rab GNPRas-related protein Rab-3A / 0.762
2gil GTPRas-related protein Rab-6A / 0.761
2rgc GNPGTPase HRas / 0.760
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.759
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.759
3pit GNPRas-related protein M-Ras / 0.758
4nyj GNPGTPase HRas / 0.757
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.757
1ky2 GNPGTP-binding protein YPT7 / 0.756
4dlx GNPGTPase HRas / 0.756
4o2l GTPGTP-binding protein Rheb / 0.755
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.754
3k9l GNPGTPase HRas / 0.754
1wdt GTPElongation factor G (EF-G-2) / 0.752
1m7b GTPRho-related GTP-binding protein RhoE / 0.751
4js0 GNPCell division control protein 42 homolog / 0.751
1d5c GDPGTPase (Rab6) / 0.749
1cxz GSPTransforming protein RhoA / 0.747
2bku GTPGTP-binding nuclear protein Ran / 0.746
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.746
3rs4 GNPGTPase HRas / 0.746
4itr GDPCell division control protein 42 homolog / 0.746
1zc3 GNPRas-related protein Ral-A / 0.744
4dls GNPGTPase HRas / 0.744
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.743
4dsu GDPGTPase KRas / 0.743
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.740
4dxa GSPRas-related protein Rap-1b / 0.739
4epx GDPGTPase KRas / 0.739
4q02 GDPGTPase KRas / 0.739
3ddc GNPGTPase HRas / 0.738
4hi0 GDPUrease accessory protein UreG / 0.738
5di3 GNPADP-ribosylation factor-like protein 3 / 0.738
1yu9 GNPRas-related protein Rab-4A / 0.737
2cls GTPRho-related GTP-binding protein Rho6 / 0.737
2gcp GSPRho-related GTP-binding protein RhoC / 0.737
4lv6 GDPGTPase KRas / 0.737
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.736
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.735
2j5x GSPADP-ribosylation factor 6 / 0.734
4mkf AP5Adenylate kinase / 0.734
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.734
4dsn GCPGTPase KRas / 0.733
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.732
4xsg GSPTransforming protein RhoA / 0.732
4fid GDPG protein alpha subunit, putative / 0.730
4y0v GDPADP-ribosylation factor 1, putative / 0.730
3lbh GNPGTPase HRas / 0.729
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.729
3kkq GDPRas-related protein M-Ras / 0.727
3nbz GTPGTP-binding nuclear protein Ran / 0.727
4epw GDPGTPase KRas / 0.727
3ea5 GDPGTP-binding nuclear protein Ran / 0.726
1wa5 GTPGTP-binding nuclear protein Ran / 0.725
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.725
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.725
1s1c GNPTransforming protein RhoA / 0.724
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.724
3x1w GDPRas-related protein Rap-1b / 0.724
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.723
4idp GNPAtlastin-1 3.6.5 0.723
4tq9 GDPGTPase KRas / 0.722
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.721
4cf7 ADPAdenylate kinase / 0.719
4wa7 GDPGTPase KRas / 0.717
2dpx GDPGTP-binding protein RAD / 0.716
1ake AP5Adenylate kinase / 0.714
2cl6 CAGGTPase HRas / 0.714
2xtn GTPGTPase IMAP family member 2 / 0.714
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.712
3oiw GNPGTPase HRas / 0.712
3tgp GNPGTPase HRas / 0.712
1g16 GDPRas-related protein SEC4 / 0.711
1z0f GDPRas-related protein Rab-14 / 0.711
1rj9 GCPSignal recognition particle receptor FtsY / 0.710
3ftq GNPSeptin-2 / 0.710
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.709
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.708
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.708
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
4qm6 GTPMetallophosphoesterase / 0.707
3ref GDPRho family GTPase / 0.706
4c2u ANPDNA helicase / 0.706
1oix GDPRas-related protein Rab-11A / 0.705
4l9w GNPGTPase HRas / 0.704
2eck ADPAdenylate kinase / 0.701
1am4 GNPCell division control protein 42 homolog / 0.700
3thy ADPDNA mismatch repair protein Msh2 / 0.700
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.699
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.699
4asu ADPATP synthase subunit alpha, mitochondrial / 0.699
4g01 GDPRas-related protein RABF2b / 0.698
4l9s GDPGTPase HRas / 0.698
4pfp ADPUnconventional myosin-VI / 0.698
5dac AGSUncharacterized protein / 0.697
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.696
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.696
3vhx GTPADP-ribosylation factor 6 / 0.696
2fe4 GDPRas-related protein Rab-6B / 0.695
4goj GNPADP-ribosylation factor-like protein 3 / 0.695
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.694
3rs0 GNPGTPase HRas / 0.692
4o2r GDPGTP-binding protein Rheb / 0.692
4qnr ATPPsp operon transcriptional activator / 0.692
1ny5 ADPTranscriptional regulator (NtrC family) / 0.691
5bn3 ADPV-type ATP synthase alpha chain / 0.691
5bn3 ADPNEQ263 / 0.691
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.691
1yra GDPGPN-loop GTPase PAB0955 / 0.690
4v02 ATPSite-determining protein / 0.690
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.688
4lhv GDPRas-related protein Rab-8A / 0.687
2r9v ATPATP synthase subunit alpha / 0.686
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.686
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.686
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.685
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.685
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.685
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.684
3q5d GDPAtlastin-1 3.6.5 0.683
4ol0 GTPGTP-binding nuclear protein Ran / 0.683
4nh0 ATPESX secretion system protein EccC / 0.682
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.681
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
2l0x GDPGTP-binding protein Rheb / 0.681
2x19 GTPGTP-binding nuclear protein GSP1/CNR1 / 0.681
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.681
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.679
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.678
3nbx ADPATPase RavA 3.6.3 0.677
4yqf GDPSeptin-9 / 0.677
2c9c ATPPsp operon transcriptional activator / 0.676
4ohx ADPProtein clpf-1 / 0.676
5fv0 ONAESX secretion system protein EccC / 0.676
2g1q ADPKinesin-like protein KIF11 / 0.675
2rgx AP5Adenylate kinase / 0.675
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.675
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.675
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.675
1yhn GTPRas-related protein Rab-7a / 0.674
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.674
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.674
4hdq GNPRas-related protein Rap-1b / 0.674
4qos ADPPsp operon transcriptional activator / 0.674
4xvq GNPGTPase HRas / 0.674
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.673
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.673
4lpk GDPGTPase KRas / 0.673
4oi2 ADPProtein clpf-1 / 0.673
4d0l GSPRas-related protein Rab-11A / 0.672
4jl6 ADPAdenylate kinase / 0.672
4uj3 GNPRas-related protein Rab-11A / 0.672
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.671
3m0e ATPTranscriptional regulator (NtrC family) / 0.671
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.671
3rs5 GNPGTPase HRas / 0.671
1a4r GNHCell division control protein 42 homolog / 0.669
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.669
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.669
3jvv ACPTwitching mobility protein / 0.669
4jl5 ADPAdenylate kinase / 0.669
4mkg AP5Adenylate kinase / 0.669
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.668
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.668
4dzz ADPPlasmid partitioning protein ParF / 0.668
4jlo ADPAdenylate kinase / 0.668
4pjj ADPUnconventional myosin-VI / 0.668
4xvr GNPGTPase HRas / 0.668
1b7t ADPMyosin heavy chain, striated muscle / 0.667
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.667
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.667
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.667
1z2a GDPRas-related protein Rab-23 / 0.667
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.667
2xto GDPGTPase IMAP family member 2 / 0.667
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.667
3pcr GTPADP-ribosylation factor 6 / 0.667
4ncl GDPEukaryotic translation initiation factor 5B / 0.667
1okk GCPSignal recognition particle protein / 0.666
1okk GCPSignal recognition particle receptor FtsY / 0.666
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.666
3wyf GTPGTP-binding nuclear protein / 0.666
4b7b ADPKinesin-like protein KIF11 / 0.666
4rkf GNPRas-related protein Rab-3 / 0.666
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.665
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.665
2rge GNPGTPase HRas / 0.664
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.664
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.664
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.663
2x7e ADPKinesin-like protein KIF11 / 0.662
3ieu GDPGTPase Era / 0.662
5cyp GSPSeptin-9 / 0.662
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.661
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
1svw GTPProbable GTP-binding protein EngB / 0.661
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.661
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
1l8q ADPChromosomal replication initiator protein DnaA / 0.660
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.660
2xsz ATPRuvB-like 2 3.6.4.12 0.660
3oes GNPGTPase RhebL1 / 0.660
3myk ANPMyosin-2 heavy chain / 0.659
3tjz GNPADP-ribosylation factor 1 / 0.659
4e03 ADPPlasmid partitioning protein ParF / 0.659
1w5s ADPORC1-type DNA replication protein 2 / 0.658
1z6t ADPApoptotic protease-activating factor 1 / 0.658
2zev B71Geranylgeranyl pyrophosphate synthase / 0.658
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.658
3tqc ADPPantothenate kinase / 0.658
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.658
4ylg GDPADP-ribosylation factor 1, putative / 0.658
2qen ADPWalker-Type ATPase / 0.657
4iij GTPTubulin alpha-1B chain / 0.657
4pk4 ADPUnconventional myosin-VI / 0.657
4ww4 ADPRuvB-like helicase / 0.657
5d3q GDPDynamin-1 3.6.5.5 0.657
2c96 ATPPsp operon transcriptional activator / 0.656
3ea0 ATPATPase, ParA family / 0.656
3hpq AP5Adenylate kinase / 0.656
3k1j ADPATP-dependent protease Lon / 0.656
3r7w GNPGTP-binding protein GTR2 / 0.656
4jld ADPAdenylate kinase / 0.656
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.656
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.655
4w5j AP5Adenylate kinase / 0.655
5fm6 ADPRuvB-like helicase / 0.655
3ffk ATPActin, alpha skeletal muscle / 0.654
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.653
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.653
3cob ADPKinesin heavy chain-like protein / 0.653
3r9i ADPSeptum site-determining protein MinD / 0.653
4mkh AP5Adenylate kinase / 0.653
1ii6 ADPKinesin-like protein KIF11 / 0.652
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.652
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.650
1svm ATPLarge T antigen 3.6.4 0.650
2fl2 ADPKinesin-like protein KIF11 / 0.650
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
3l9h ADPKinesin-like protein KIF11 / 0.650