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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
1oyy AGS ATP-dependent DNA helicase RecQ 3.6.4.12

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1oyy AGSATP-dependent DNA helicase RecQ 3.6.4.12 1.059
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.711
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.710
2c5l GTPGTPase HRas / 0.708
3tgp GNPGTPase HRas / 0.708
4idp GNPAtlastin-1 3.6.5 0.706
5l3s GNPSignal recognition particle receptor FtsY / 0.703
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.702
5bn3 ADPV-type ATP synthase alpha chain / 0.702
5bn3 ADPNEQ263 / 0.702
4idn GNPAtlastin-1 3.6.5 0.700
3w3z GTPGTP-binding nuclear protein Ran / 0.699
3i3s GNPGTPase HRas / 0.697
3k8y GNPGTPase HRas / 0.697
3rs4 GNPGTPase HRas / 0.697
3rs5 GNPGTPase HRas / 0.697
3rs7 GNPGTPase HRas / 0.697
3v4f GNPGTPase HRas / 0.697
4lhv GDPRas-related protein Rab-8A / 0.697
4hdo GNPRas-related protein Rap-1b / 0.695
3q5d GDPAtlastin-1 3.6.5 0.694
4nyj GNPGTPase HRas / 0.694
2d7d ADPUvrABC system protein B / 0.693
4ys0 ADPProtein translocase subunit SecA / 0.693
1zc3 GNPRas-related protein Ral-A / 0.692
4g0n GNPGTPase HRas / 0.692
3x1z GNPRas-related protein Rap-1b / 0.690
3zfd ANPChromosome-associated kinesin KIF4 / 0.690
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.690
1z2a GDPRas-related protein Rab-23 / 0.689
3bxz ADPProtein translocase subunit SecA / 0.689
1esn ANPPantothenate kinase 2.7.1.33 0.688
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.686
3tso GNPRas-related protein Rab-25 / 0.686
2bme GNPRas-related protein Rab-4A / 0.684
3oiu GNPGTPase HRas / 0.684
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.683
2rgb GNPGTPase HRas / 0.683
2rge GNPGTPase HRas / 0.683
2rgg GNPGTPase HRas / 0.683
3ddc GNPGTPase HRas / 0.683
4l9w GNPGTPase HRas / 0.683
1okk GCPSignal recognition particle protein / 0.682
1okk GCPSignal recognition particle receptor FtsY / 0.682
2whx ADPGenome polyprotein 3.4.21.91 0.682
3lbh GNPGTPase HRas / 0.682
3oiv GNPGTPase HRas / 0.682
3oiw GNPGTPase HRas / 0.682
3rs0 GNPGTPase HRas / 0.682
3rsl GNPGTPase HRas / 0.682
4a28 ADPKinesin-like protein KIF11 / 0.682
4cdg ADPBloom syndrome protein 3.6.4.12 0.682
4dlv GNPGTPase HRas / 0.682
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.682
2gil GTPRas-related protein Rab-6A / 0.681
2j7p GNPSignal recognition particle protein / 0.681
2j7p GNPSignal recognition particle receptor FtsY / 0.681
3bc1 GNPRas-related protein Rab-27A / 0.681
5b2z GNPGTPase HRas / 0.681
5jlj GNPGTP-binding nuclear protein Ran / 0.681
3l8y GNPGTPase HRas / 0.680
1x1r GDPRas-related protein M-Ras / 0.679
3tjz GNPADP-ribosylation factor 1 / 0.679
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.678
4xvq GNPGTPase HRas / 0.678
1ii6 ADPKinesin-like protein KIF11 / 0.677
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.676
2fe4 GDPRas-related protein Rab-6B / 0.676
3kkq GDPRas-related protein M-Ras / 0.676
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.676
4lv6 GDPGTPase KRas / 0.676
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.675
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.675
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.675
1ow3 GDPTransforming protein RhoA / 0.674
3cph GDPRas-related protein SEC4 / 0.674
4ql3 GDPGTPase KRas / 0.674
4xvr GNPGTPase HRas / 0.674
4dlt GNPGTPase HRas / 0.673
4q02 GDPGTPase KRas / 0.673
1d5c GDPGTPase (Rab6) / 0.672
1rj9 GCPSignal recognition particle receptor FtsY / 0.672
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
3q9l ATPSeptum site-determining protein MinD / 0.672
4lrw GDPGTPase KRas / 0.672
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.672
1n6m ADPProtein claret segregational / 0.670
2bku GTPGTP-binding nuclear protein Ran / 0.670
4dlw GNPGTPase HRas / 0.670
4q03 GDPGTPase KRas / 0.670
1l8q ADPChromosomal replication initiator protein DnaA / 0.669
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.669
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.669
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.669
3lbi GNPGTPase HRas / 0.669
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.669
4nyi GNPGTPase HRas / 0.669
5dif GNPGTP-binding nuclear protein Ran / 0.669
1k5d GNPGTP-binding nuclear protein Ran / 0.668
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.668
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
2pg2 ADPKinesin-like protein KIF11 / 0.668
4luc GDPGTPase KRas / 0.668
5aun ADPIron-sulfur cluster carrier protein / 0.668
2fg5 GNPRas-related protein Rab-31 / 0.667
2x2r ADPKinesin-like protein KIF11 / 0.667
3lbn GNPGTPase HRas / 0.667
4o3m ADPBloom syndrome protein 3.6.4.12 0.667
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.666
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.666
1nsf ATPVesicle-fusing ATPase 3.6.4.6 0.666
1xtr GNPGTP-binding protein Rheb / 0.666
2fna ADPUncharacterized protein / 0.666
3e5h GNPRas-related protein Rab-28 / 0.666
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.666
4dls GNPGTPase HRas / 0.666
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.665
3pit GNPRas-related protein M-Ras / 0.665
2gcp GSPRho-related GTP-binding protein RhoC / 0.664
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.664
2uyi ADPKinesin-like protein KIF11 / 0.664
4cym GCPRas-related protein Rab-32 / 0.664
4wa7 GDPGTPase KRas / 0.664
1b7t ADPMyosin heavy chain, striated muscle / 0.663
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.663
1sxj AGSReplication factor C subunit 1 / 0.662
3mjh GTPRas-related protein Rab-5A / 0.662
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.661
3dyl IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A / 0.661
3kz1 GSPTransforming protein RhoA / 0.661
4dlx GNPGTPase HRas / 0.661
4dzz ADPPlasmid partitioning protein ParF / 0.661
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.661
1ibr GNPGTP-binding nuclear protein Ran / 0.660
1ky2 GNPGTP-binding protein YPT7 / 0.660
2zrj AGSProtein RecA / 0.660
3hqd ANPKinesin-like protein KIF11 / 0.660
4l8g GDPGTPase KRas / 0.660
1nly AGSCag alpha / 0.659
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.659
4js0 GNPCell division control protein 42 homolog / 0.659
4pjk ADPMyosin-2 heavy chain / 0.659
1w5t ANPORC1-type DNA replication protein 2 / 0.658
2a3b CFFEndochitinase B1 3.2.1.14 0.658
4l9s GDPGTPase HRas / 0.658
1f5n GNPGuanylate-binding protein 1 / 0.657
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.657
3kuc GDPRas-related protein Rap-1A / 0.657
1m67 BOAGlycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal 1.1.1.8 0.656
1yu9 GNPRas-related protein Rab-4A / 0.656
2uz3 TTPThymidine kinase / 0.656
4dxa GSPRas-related protein Rap-1b / 0.656
4v02 ATPSite-determining protein / 0.656
1v8k ANPKinesin-like protein KIF2C / 0.655
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.654
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.654
1g16 GDPRas-related protein SEC4 / 0.654
4gp6 ADPMetallophosphoesterase / 0.654
1mmg AGSMyosin-2 heavy chain / 0.653
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.653
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
2qen ADPWalker-Type ATPase / 0.653
4kvg GTPRas-related protein Rap-1A / 0.653
4uj3 GNPRas-related protein Rab-11A / 0.653
1fnn ADPORC1-type DNA replication protein / 0.652
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.652
4ncl GDPEukaryotic translation initiation factor 5B / 0.652
4pfp ADPUnconventional myosin-VI / 0.652
4xvu ATPATPase GET3 / 0.652
5di3 GNPADP-ribosylation factor-like protein 3 / 0.652
2cl6 CAGGTPase HRas / 0.651
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
2xae ADPKinesin-like protein KIF11 / 0.650
3l1c ADPProtein claret segregational / 0.650
3myk ANPMyosin-2 heavy chain / 0.650