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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
2ad5 ADP CTP synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ad5 ADPCTP synthase / 0.969
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.729
1p9w ANPType II secretion system protein E / 0.725
3ref GDPRho family GTPase / 0.723
5aun ADPIron-sulfur cluster carrier protein / 0.722
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.718
1ny5 ADPTranscriptional regulator (NtrC family) / 0.717
4itr GDPCell division control protein 42 homolog / 0.717
4dvg GSPRho family GTPase / 0.715
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.710
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.709
4qos ADPPsp operon transcriptional activator / 0.709
4xoi GTPTransforming protein RhoA / 0.709
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.706
4jjz ADPFormate--tetrahydrofolate ligase / 0.706
1cxz GSPTransforming protein RhoA / 0.705
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.704
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.704
3oes GNPGTPase RhebL1 / 0.704
1z0a GDPRas-related protein Rab-2A / 0.702
1x1r GDPRas-related protein M-Ras / 0.701
1z0f GDPRas-related protein Rab-14 / 0.701
3kkq GDPRas-related protein M-Ras / 0.701
4ql3 GDPGTPase KRas / 0.700
2c96 ATPPsp operon transcriptional activator / 0.699
3rs0 GNPGTPase HRas / 0.698
1kmq GNPTransforming protein RhoA / 0.697
1a2b GSPTransforming protein RhoA / 0.696
1wbb ADPDNA mismatch repair protein MutS / 0.696
1z0d GDPRas-related protein Rab-5C / 0.696
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.696
2qen ADPWalker-Type ATPase / 0.696
1oix GDPRas-related protein Rab-11A / 0.695
2y65 ADPKinesin heavy chain / 0.695
4epx GDPGTPase KRas / 0.695
1sdm ADPKinesin heavy chain-like protein / 0.694
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.693
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.692
4dso GSPGTPase KRas / 0.692
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.691
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.691
3kko GNPRas-related protein M-Ras / 0.691
4wa7 GDPGTPase KRas / 0.690
1mmg AGSMyosin-2 heavy chain / 0.688
4epw GDPGTPase KRas / 0.688
1rrg GDPADP-ribosylation factor 1 / 0.687
2ce2 GDPGTPase HRas / 0.687
4q03 GDPGTPase KRas / 0.687
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.686
3lbh GNPGTPase HRas / 0.686
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.685
3kuc GDPRas-related protein Rap-1A / 0.685
4dsu GDPGTPase KRas / 0.685
4q02 GDPGTPase KRas / 0.684
2fna ADPUncharacterized protein / 0.683
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.683
4l9s GDPGTPase HRas / 0.683
1xtr GNPGTP-binding protein Rheb / 0.682
2c5l GTPGTPase HRas / 0.682
4g0n GNPGTPase HRas / 0.682
4o2l GTPGTP-binding protein Rheb / 0.682
3rs4 GNPGTPase HRas / 0.681
4kvg GTPRas-related protein Rap-1A / 0.681
4l8g GDPGTPase KRas / 0.681
4lv6 GDPGTPase KRas / 0.681
3kz1 GSPTransforming protein RhoA / 0.680
3oiw GNPGTPase HRas / 0.680
4o3m ADPBloom syndrome protein 3.6.4.12 0.680
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.679
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
3myk ANPMyosin-2 heavy chain / 0.679
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.679
4lhv GDPRas-related protein Rab-8A / 0.679
4dlw GNPGTPase HRas / 0.678
4dzz ADPPlasmid partitioning protein ParF / 0.678
4yqf GDPSeptin-9 / 0.678
3rab GNPRas-related protein Rab-3A / 0.677
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.677
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.675
1ow3 GDPTransforming protein RhoA / 0.675
1wa5 GTPGTP-binding nuclear protein Ran / 0.675
3rs5 GNPGTPase HRas / 0.675
4nyj GNPGTPase HRas / 0.675
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.674
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.674
1svw GTPProbable GTP-binding protein EngB / 0.674
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.674
4hse ADPChaperone protein ClpB / 0.674
4pjk ADPMyosin-2 heavy chain / 0.674
4ys0 ADPProtein translocase subunit SecA / 0.674
1b7t ADPMyosin heavy chain, striated muscle / 0.673
1fmw ATPMyosin-2 heavy chain / 0.673
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.673
5ftf ADPTPR domain protein / 0.673
1e4y AP5Adenylate kinase / 0.672
1mma ADPMyosin-2 heavy chain / 0.672
2gil GTPRas-related protein Rab-6A / 0.672
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.672
3a6p GTPGTP-binding nuclear protein Ran / 0.672
4obe GDPGTPase KRas / 0.672
3a58 GNPGTP-binding protein RHO1 / 0.671
3ddc GNPGTPase HRas / 0.671
4dxa GSPRas-related protein Rap-1b / 0.671
4ldj GDPGTPase KRas / 0.671
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.670
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.670
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.670
3x1w GDPRas-related protein Rap-1b / 0.670
2pg2 ADPKinesin-like protein KIF11 / 0.669
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.669
3k8y GNPGTPase HRas / 0.669
3pcr GTPADP-ribosylation factor 6 / 0.669
3pit GNPRas-related protein M-Ras / 0.669
4asu ADPATP synthase subunit alpha, mitochondrial / 0.669
4tq9 GDPGTPase KRas / 0.669
5ftc ADPTPR domain protein / 0.669
3kud GDPGTPase HRas / 0.668
3x1z GNPRas-related protein Rap-1b / 0.668
1z2a GDPRas-related protein Rab-23 / 0.667
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.667
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.667
4b7b ADPKinesin-like protein KIF11 / 0.667
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.666
2uyi ADPKinesin-like protein KIF11 / 0.666
2x2r ADPKinesin-like protein KIF11 / 0.666
3i3s GNPGTPase HRas / 0.666
1g16 GDPRas-related protein SEC4 / 0.665
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.665
4v02 ATPSite-determining protein / 0.665
2gcp GSPRho-related GTP-binding protein RhoC / 0.664
3eg5 GNPCell division control protein 42 homolog / 0.664
4js0 GNPCell division control protein 42 homolog / 0.664
1d5c GDPGTPase (Rab6) / 0.663
1g17 GNPRas-related protein SEC4 / 0.663
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.663
1rj9 GCPSignal recognition particle receptor FtsY / 0.663
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.663
3cph GDPRas-related protein SEC4 / 0.663
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.663
4rkf GNPRas-related protein Rab-3 / 0.663
5fl3 ADPPili retraction protein PilT / 0.663
1gwn GTPRho-related GTP-binding protein RhoE / 0.662
1m7b GTPRho-related GTP-binding protein RhoE / 0.662
4luc GDPGTPase KRas / 0.662
1uad GNPRas-related protein Ral-A / 0.661
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.661
4lpk GDPGTPase KRas / 0.661
4ol0 GTPGTP-binding nuclear protein Ran / 0.661
1lfd GNPGTPase HRas / 0.660
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.660
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.659
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.659
5bn3 ADPV-type ATP synthase alpha chain / 0.659
5bn3 ADPNEQ263 / 0.659
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.658
4cdg ADPBloom syndrome protein 3.6.4.12 0.658
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.658
1a4r GNHCell division control protein 42 homolog / 0.657
1yra GDPGPN-loop GTPase PAB0955 / 0.657
4x8o AP5Adenylate kinase / 0.657
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.656
1fnn ADPORC1-type DNA replication protein / 0.656
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.656
1yzq GNPRas-related protein Rab-6A / 0.656
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
3k9l GNPGTPase HRas / 0.656
3m0e ATPTranscriptional regulator (NtrC family) / 0.656
4hdq GNPRas-related protein Rap-1b / 0.656
4ncl GDPEukaryotic translation initiation factor 5B / 0.656
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.655
1w5s ADPORC1-type DNA replication protein 2 / 0.654
2v7u SAM5'-fluoro-5'-deoxy-adenosine synthase / 0.654
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
2q2z ADPKinesin-like protein KIF11 / 0.653
3tqc ADPPantothenate kinase / 0.653
4dlz GNPGTPase HRas / 0.653
4iei ADPGene 2 protein / 0.653
1z6t ADPApoptotic protease-activating factor 1 / 0.652
2fe4 GDPRas-related protein Rab-6B / 0.652
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
2rgb GNPGTPase HRas / 0.651
3mjh GTPRas-related protein Rab-5A / 0.651
3oiv GNPGTPase HRas / 0.651
3r9i ADPSeptum site-determining protein MinD / 0.651
4qbi AP5Adenylate kinase / 0.651
4xvq GNPGTPase HRas / 0.651
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.650
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.650
1k5d GNPGTP-binding nuclear protein Ran / 0.650
2ffq GSPRas-related protein Rab-6B / 0.650
3ea5 GDPGTP-binding nuclear protein Ran / 0.650
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.650
4hdo GNPRas-related protein Rap-1b / 0.650
4xsg GSPTransforming protein RhoA / 0.650