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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
3uk6 ADP RuvB-like 2 3.6.4.12

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3uk6 ADPRuvB-like 2 3.6.4.12 1.108
4ww4 ADPRuvB-like helicase / 0.924
2xsz ATPRuvB-like 2 3.6.4.12 0.877
2c9o ADPRuvB-like 1 3.6.4.12 0.801
5fl3 ADPPili retraction protein PilT / 0.764
4zca ADPKinesin-like protein KIF11 / 0.749
5fm6 ADPRuvB-like helicase / 0.741
4asu ADPATP synthase subunit alpha, mitochondrial / 0.738
2gm1 ADPKinesin-like protein KIF11 / 0.737
3k1j ADPATP-dependent protease Lon / 0.737
2ql6 ADPNicotinamide riboside kinase 1 / 0.734
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.734
1l8q ADPChromosomal replication initiator protein DnaA / 0.733
2q2z ADPKinesin-like protein KIF11 / 0.729
2y65 ADPKinesin heavy chain / 0.726
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.723
1fmw ATPMyosin-2 heavy chain / 0.722
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.722
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.721
4b7b ADPKinesin-like protein KIF11 / 0.721
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.721
2ffq GSPRas-related protein Rab-6B / 0.720
3nbx ADPATPase RavA 3.6.3 0.718
4x8l AP5Adenylate kinase / 0.718
2c9c ATPPsp operon transcriptional activator / 0.716
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.715
1fnn ADPORC1-type DNA replication protein / 0.714
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.713
2r9v ATPATP synthase subunit alpha / 0.713
1mma ADPMyosin-2 heavy chain / 0.711
2zr9 DTPProtein RecA / 0.708
3bbp GTPRas-related protein Rab-6A / 0.706
4x8o AP5Adenylate kinase / 0.701
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.699
2eck ADPAdenylate kinase / 0.698
3ftq GNPSeptin-2 / 0.698
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.697
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.695
1rrg GDPADP-ribosylation factor 1 / 0.693
1z0f GDPRas-related protein Rab-14 / 0.691
1tu3 GNPRas-related protein Rab-5A / 0.690
2hld ANPATP synthase subunit alpha, mitochondrial / 0.690
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.689
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.689
5aun ADPIron-sulfur cluster carrier protein / 0.689
4pk4 ADPUnconventional myosin-VI / 0.687
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.686
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.685
3kud GDPGTPase HRas / 0.685
4g0n GNPGTPase HRas / 0.685
3a6p GTPGTP-binding nuclear protein Ran / 0.684
5ftf ADPTPR domain protein / 0.684
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.683
1wdt GTPElongation factor G (EF-G-2) / 0.683
2c5l GTPGTPase HRas / 0.683
3hpr AP5Adenylate kinase / 0.682
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.681
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.681
3t1t GDPProbable gliding protein mglA / 0.679
4ihq ADPConserved Archaeal protein / 0.678
1e4y AP5Adenylate kinase / 0.677
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.677
4cym GCPRas-related protein Rab-32 / 0.676
4i1v ADPDephospho-CoA kinase / 0.675
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.674
4pfp ADPUnconventional myosin-VI / 0.674
1a2b GSPTransforming protein RhoA / 0.673
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.673
3cph GDPRas-related protein SEC4 / 0.672
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.672
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.672
1w5s ADPORC1-type DNA replication protein 2 / 0.671
3x1w GDPRas-related protein Rap-1b / 0.670
5fm7 ADPRuvB-like helicase / 0.670
1xts GTPGTP-binding protein Rheb / 0.669
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.669
4kvg GTPRas-related protein Rap-1A / 0.669
1uad GNPRas-related protein Ral-A / 0.668
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.668
4qnr ATPPsp operon transcriptional activator / 0.667
4xoi GTPTransforming protein RhoA / 0.667
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.666
2zrj AGSProtein RecA / 0.666
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.666
3tqc ADPPantothenate kinase / 0.666
4qbi AP5Adenylate kinase / 0.666
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.665
1ii6 ADPKinesin-like protein KIF11 / 0.665
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.665
2bc9 GNPGuanylate-binding protein 1 / 0.664
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.664
5ftc ADPTPR domain protein / 0.664
1g41 ADPATP-dependent protease ATPase subunit HslU / 0.663
3a58 GNPGTP-binding protein RHO1 / 0.663
3tgp GNPGTPase HRas / 0.663
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.662
2pg2 ADPKinesin-like protein KIF11 / 0.662
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.661
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.661
4l16 ADPFidgetin-like protein 1 3.6.4 0.661
4q03 GDPGTPase KRas / 0.661
1g6o ADPCag alpha / 0.659
4qbg AP5Adenylate kinase / 0.659
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.658
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.658
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.658
1lfd GNPGTPase HRas / 0.657
1yzq GNPRas-related protein Rab-6A / 0.657
2vf7 ADPUvrABC system protein A / 0.657
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.657
1b7t ADPMyosin heavy chain, striated muscle / 0.655
1svl ADPLarge T antigen 3.6.4 0.655
4jjz ADPFormate--tetrahydrofolate ligase / 0.655
4qxa GTPRas-related protein Rab-9A / 0.655
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.655
4d81 ADPAAA ATPase, central domain protein / 0.654
4xvq GNPGTPase HRas / 0.654
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.653
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.653
1zc3 GNPRas-related protein Ral-A / 0.652
3pcr GTPADP-ribosylation factor 6 / 0.652
4lrw GDPGTPase KRas / 0.652
4jky ADPAdenylate kinase / 0.651
1e4v AP5Adenylate kinase / 0.650
1p3j AP5Adenylate kinase / 0.650
4mkf AP5Adenylate kinase / 0.650