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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
1ht2 ADP ATP-dependent protease ATPase subunit HslU

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1ht2 ADPATP-dependent protease ATPase subunit HslU / 1.009
1g41 ADPATP-dependent protease ATPase subunit HslU / 0.806
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.780
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.747
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.745
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.743
2q2z ADPKinesin-like protein KIF11 / 0.730
4qos ADPPsp operon transcriptional activator / 0.721
3uk6 ADPRuvB-like 2 3.6.4.12 0.713
3d8b ADPFidgetin-like protein 1 3.6.4 0.712
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.709
2pg2 ADPKinesin-like protein KIF11 / 0.709
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.709
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.704
3l9h ADPKinesin-like protein KIF11 / 0.704
1l8q ADPChromosomal replication initiator protein DnaA / 0.703
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.703
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.702
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.702
2x7e ADPKinesin-like protein KIF11 / 0.702
5fl3 ADPPili retraction protein PilT / 0.702
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.699
3t1t GDPProbable gliding protein mglA / 0.697
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.697
2fl2 ADPKinesin-like protein KIF11 / 0.696
2c9o ADPRuvB-like 1 3.6.4.12 0.695
1g16 GDPRas-related protein SEC4 / 0.694
3zia ATPATP synthase subunit alpha, mitochondrial / 0.694
4yqf GDPSeptin-9 / 0.693
2uyi ADPKinesin-like protein KIF11 / 0.692
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.692
2xsz ATPRuvB-like 2 3.6.4.12 0.692
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.691
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.690
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.690
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.688
1z0a GDPRas-related protein Rab-2A / 0.687
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.687
3a58 GNPGTP-binding protein RHO1 / 0.685
3r9i ADPSeptum site-determining protein MinD / 0.685
1e4v AP5Adenylate kinase / 0.684
4l8g GDPGTPase KRas / 0.684
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.683
5cyo GDPSeptin-9 / 0.683
1x1r GDPRas-related protein M-Ras / 0.682
2cea ADPATP-dependent zinc metalloprotease FtsH / 0.682
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.682
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.682
3kkq GDPRas-related protein M-Ras / 0.682
4l9s GDPGTPase HRas / 0.682
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.681
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.681
3x1w GDPRas-related protein Rap-1b / 0.681
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.681
4epx GDPGTPase KRas / 0.681
4q02 GDPGTPase KRas / 0.681
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.680
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.680
4gp6 ADPMetallophosphoesterase / 0.680
4tq9 GDPGTPase KRas / 0.680
4wa7 GDPGTPase KRas / 0.680
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.679
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
1s1c GNPTransforming protein RhoA / 0.679
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.679
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
1zc3 GNPRas-related protein Ral-A / 0.679
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.679
1fnn ADPORC1-type DNA replication protein / 0.678
1kmq GNPTransforming protein RhoA / 0.678
1ny5 ADPTranscriptional regulator (NtrC family) / 0.678
1z2a GDPRas-related protein Rab-23 / 0.678
4dlz GNPGTPase HRas / 0.678
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.678
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.677
4lv6 GDPGTPase KRas / 0.677
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.676
1z0d GDPRas-related protein Rab-5C / 0.676
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.676
3c41 ANPAmino acid ABC transporter / 0.676
4a1z ADPKinesin-like protein KIF11 / 0.676
4epw GDPGTPase KRas / 0.676
4q03 GDPGTPase KRas / 0.675
4ql3 GDPGTPase KRas / 0.675
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.675
5hpy GDPTransforming protein RhoA / 0.675
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.674
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.674
4kod ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.674
1yzq GNPRas-related protein Rab-6A / 0.673
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.672
5bn3 ADPV-type ATP synthase alpha chain / 0.672
5bn3 ADPNEQ263 / 0.672
2y65 ADPKinesin heavy chain / 0.671
4b7b ADPKinesin-like protein KIF11 / 0.671
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.670
2qen ADPWalker-Type ATPase / 0.669
4dlw GNPGTPase HRas / 0.669
1g17 GNPRas-related protein SEC4 / 0.667
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.667
1w5t ADPORC1-type DNA replication protein 2 / 0.667
1yrs ADPKinesin-like protein KIF11 / 0.667
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.667
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
3eg5 GNPCell division control protein 42 homolog / 0.667
4xoi GTPTransforming protein RhoA / 0.667
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.666
1sdm ADPKinesin heavy chain-like protein / 0.666
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.666
2l0x GDPGTP-binding protein Rheb / 0.666
4fcw ADPChaperone protein ClpB / 0.666
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.665
2zrj AGSProtein RecA / 0.665
3k1j ADPATP-dependent protease Lon / 0.665
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.665
3oiw GNPGTPase HRas / 0.665
4hi0 GDPUrease accessory protein UreG / 0.665
4i1v ADPDephospho-CoA kinase / 0.665
2ce2 GDPGTPase HRas / 0.664
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.664
2rgb GNPGTPase HRas / 0.664
4dlv GNPGTPase HRas / 0.664
1svl ADPLarge T antigen 3.6.4 0.663
2r9v ATPATP synthase subunit alpha / 0.663
3ddc GNPGTPase HRas / 0.663
3kud GDPGTPase HRas / 0.663
3tqc ADPPantothenate kinase / 0.663
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.662
2dpx GDPGTP-binding protein RAD / 0.662
2ffq GSPRas-related protein Rab-6B / 0.662
3l8y GNPGTPase HRas / 0.662
3tgp GNPGTPase HRas / 0.662
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.662
4l9w GNPGTPase HRas / 0.662
4pk4 ADPUnconventional myosin-VI / 0.662
1e4y AP5Adenylate kinase / 0.661
1rrg GDPADP-ribosylation factor 1 / 0.661
2gil GTPRas-related protein Rab-6A / 0.661
3lbh GNPGTPase HRas / 0.661
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.661
2fe4 GDPRas-related protein Rab-6B / 0.660
3lbi GNPGTPase HRas / 0.660
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.660
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.660
1am4 GNPCell division control protein 42 homolog / 0.659
2ad5 ADPCTP synthase / 0.659
3cob ADPKinesin heavy chain-like protein / 0.659
3q5d GDPAtlastin-1 3.6.5 0.659
4idn GNPAtlastin-1 3.6.5 0.659
4lhv GDPRas-related protein Rab-8A / 0.659
3x1z GNPRas-related protein Rap-1b / 0.658
4xvq GNPGTPase HRas / 0.658
3tlx ADPAdenylate kinase 2 / 0.657
4z54 GDPNeuronal-specific septin-3 / 0.657
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.656
1ow3 GDPTransforming protein RhoA / 0.656
2eck ADPAdenylate kinase / 0.656
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.656
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.656
3ref GDPRho family GTPase / 0.656
4hdo GNPRas-related protein Rap-1b / 0.656
4idp GNPAtlastin-1 3.6.5 0.656
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.655
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.655
2osb AP5Adenylate kinase / 0.655
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.655
5b2z GNPGTPase HRas / 0.655
1jx2 ADPMyosin-2 heavy chain / 0.654
1xmv ADPProtein RecA / 0.654
3oiv GNPGTPase HRas / 0.654
5ftc ADPTPR domain protein / 0.654
1vg8 GNPRas-related protein Rab-7a / 0.653
2c96 ATPPsp operon transcriptional activator / 0.653
2gm1 ADPKinesin-like protein KIF11 / 0.653
4asu ADPATP synthase subunit alpha, mitochondrial / 0.653
4d81 ADPAAA ATPase, central domain protein / 0.653
4iok ADPFormate--tetrahydrofolate ligase / 0.653
4nyj GNPGTPase HRas / 0.653
4pfp ADPUnconventional myosin-VI / 0.653
1cxz GSPTransforming protein RhoA / 0.652
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.652
3rsl GNPGTPase HRas / 0.652
4js0 GNPCell division control protein 42 homolog / 0.652
4nl4 ADPPrimosomal protein N' / 0.652
4qm6 GTPMetallophosphoesterase / 0.652
1lfd GNPGTPase HRas / 0.651
2gcp GSPRho-related GTP-binding protein RhoC / 0.651
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.651
3pit GNPRas-related protein M-Ras / 0.651
3rs4 GNPGTPase HRas / 0.651
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.651
3v4f GNPGTPase HRas / 0.651
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.650
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
3kko GNPRas-related protein M-Ras / 0.650