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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
1s3s ADP Transitional endoplasmic reticulum ATPase 3.6.4.6

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.965
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.865
3k1j ADPATP-dependent protease Lon / 0.789
4d81 ADPAAA ATPase, central domain protein / 0.785
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.748
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.744
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.744
4kod ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.743
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.739
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.738
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.724
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.724
3t1t GDPProbable gliding protein mglA / 0.723
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.718
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.718
1ow3 GDPTransforming protein RhoA / 0.717
4y0v GDPADP-ribosylation factor 1, putative / 0.717
4ylg GDPADP-ribosylation factor 1, putative / 0.717
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.716
1gwn GTPRho-related GTP-binding protein RhoE / 0.716
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.714
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.714
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.714
2y65 ADPKinesin heavy chain / 0.714
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.713
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.713
5bn3 ADPV-type ATP synthase alpha chain / 0.713
5bn3 ADPNEQ263 / 0.713
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.712
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.710
4jlo ADPAdenylate kinase / 0.710
3kud GDPGTPase HRas / 0.709
4qbi AP5Adenylate kinase / 0.707
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.706
3d8b ADPFidgetin-like protein 1 3.6.4 0.706
3r9i ADPSeptum site-determining protein MinD / 0.706
4pjk ADPMyosin-2 heavy chain / 0.706
4pjj ADPUnconventional myosin-VI / 0.705
1sq5 ADPPantothenate kinase 2.7.1.33 0.704
2fe4 GDPRas-related protein Rab-6B / 0.704
3kuc GDPRas-related protein Rap-1A / 0.704
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.703
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.703
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.703
2cea ADPATP-dependent zinc metalloprotease FtsH / 0.703
4dxa GSPRas-related protein Rap-1b / 0.703
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.702
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.702
1d5c GDPGTPase (Rab6) / 0.701
4dso GSPGTPase KRas / 0.701
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.700
1z0d GDPRas-related protein Rab-5C / 0.700
4l9s GDPGTPase HRas / 0.700
4obe GDPGTPase KRas / 0.700
4jky ADPAdenylate kinase / 0.699
1t91 GTPRas-related protein Rab-7a / 0.698
2bku GTPGTP-binding nuclear protein Ran / 0.698
4epw GDPGTPase KRas / 0.698
4lv6 GDPGTPase KRas / 0.698
1zbd GTPRas-related protein Rab-3A / 0.697
3x1w GDPRas-related protein Rap-1b / 0.697
4ql3 GDPGTPase KRas / 0.697
4tq9 GDPGTPase KRas / 0.697
4xgu ADPPutative pachytene checkpoint protein 2 / 0.697
3cf0 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.696
3l9h ADPKinesin-like protein KIF11 / 0.696
4ldj GDPGTPase KRas / 0.696
4q03 GDPGTPase KRas / 0.696
4wa7 GDPGTPase KRas / 0.696
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.696
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.695
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
2ce2 GDPGTPase HRas / 0.695
4q02 GDPGTPase KRas / 0.695
4qbh AP5Adenylate kinase / 0.695
1sdm ADPKinesin heavy chain-like protein / 0.694
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.694
2gm1 ADPKinesin-like protein KIF11 / 0.694
3nbx ADPATPase RavA 3.6.3 0.694
4dsu GDPGTPase KRas / 0.694
4epx GDPGTPase KRas / 0.694
3m0e ATPTranscriptional regulator (NtrC family) / 0.693
4b7b ADPKinesin-like protein KIF11 / 0.693
4cf7 ADPAdenylate kinase / 0.693
2pg2 ADPKinesin-like protein KIF11 / 0.692
2uyi ADPKinesin-like protein KIF11 / 0.692
4gp6 ADPMetallophosphoesterase / 0.692
4l8g GDPGTPase KRas / 0.692
2x2r ADPKinesin-like protein KIF11 / 0.691
2xae ADPKinesin-like protein KIF11 / 0.691
5cyo GDPSeptin-9 / 0.691
1e4v AP5Adenylate kinase / 0.690
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.690
4ihq ADPConserved Archaeal protein / 0.690
2zro ADPProtein RecA / 0.689
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.689
4idn GNPAtlastin-1 3.6.5 0.689
1mma ADPMyosin-2 heavy chain / 0.688
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.687
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.687
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.687
2x7e ADPKinesin-like protein KIF11 / 0.687
4x8o AP5Adenylate kinase / 0.687
1a2b GSPTransforming protein RhoA / 0.686
1yrs ADPKinesin-like protein KIF11 / 0.686
2fl2 ADPKinesin-like protein KIF11 / 0.686
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.686
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.685
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.683
4lhv GDPRas-related protein Rab-8A / 0.683
4o25 GTPGTP-binding protein Rheb / 0.683
5fl3 ADPPili retraction protein PilT / 0.683
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.682
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.682
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.682
3tjz GNPADP-ribosylation factor 1 / 0.682
4qxa GTPRas-related protein Rab-9A / 0.682
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.681
1wdt GTPElongation factor G (EF-G-2) / 0.681
4lpk GDPGTPase KRas / 0.681
1p3j AP5Adenylate kinase / 0.680
2dpx GDPGTP-binding protein RAD / 0.680
3zia ATPATP synthase subunit alpha, mitochondrial / 0.680
1oix GDPRas-related protein Rab-11A / 0.679
1svl ADPLarge T antigen 3.6.4 0.679
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.679
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.678
2rgx AP5Adenylate kinase / 0.678
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.678
4qbg AP5Adenylate kinase / 0.678
2dr3 ADPUPF0273 protein PH0284 / 0.677
4hi0 GDPUrease accessory protein UreG / 0.677
4iei ADPGene 2 protein / 0.677
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.677
4z54 GDPNeuronal-specific septin-3 / 0.677
5dha GNPGTP-binding nuclear protein Ran / 0.677
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.676
2whx ADPGenome polyprotein 3.4.21.91 0.676
3l1c ADPProtein claret segregational / 0.676
1b7t ADPMyosin heavy chain, striated muscle / 0.674
4jl5 ADPAdenylate kinase / 0.673
1m7b GTPRho-related GTP-binding protein RhoE / 0.672
3cph GDPRas-related protein SEC4 / 0.672
4idp GNPAtlastin-1 3.6.5 0.672
4pfp ADPUnconventional myosin-VI / 0.672
5ftc ADPTPR domain protein / 0.672
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.671
1jx2 ADPMyosin-2 heavy chain / 0.671
3a58 GNPGTP-binding protein RHO1 / 0.671
3ea5 GDPGTP-binding nuclear protein Ran / 0.671
3hpq AP5Adenylate kinase / 0.671
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
4a28 ADPKinesin-like protein KIF11 / 0.671
4ap0 ADPKinesin-like protein KIF11 / 0.671
4luc GDPGTPase KRas / 0.671
4ncl GDPEukaryotic translation initiation factor 5B / 0.671
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.670
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.670
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.670
2zr9 DTPProtein RecA / 0.670
2zrj AGSProtein RecA / 0.670
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.670
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.669
1l8q ADPChromosomal replication initiator protein DnaA / 0.669
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.669
4xvq GNPGTPase HRas / 0.669
1kmq GNPTransforming protein RhoA / 0.668
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.668
3q5d GDPAtlastin-1 3.6.5 0.668
1wa5 GTPGTP-binding nuclear protein Ran / 0.667
2cl6 CAGGTPase HRas / 0.667
2ql6 ADPNicotinamide riboside kinase 1 / 0.667
1v8k ANPKinesin-like protein KIF2C / 0.666
3ddc GNPGTPase HRas / 0.666
3zfd ANPChromosome-associated kinesin KIF4 / 0.666
4zca ADPKinesin-like protein KIF11 / 0.666
1fnn ADPORC1-type DNA replication protein / 0.665
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.665
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.665
1zio AP5Adenylate kinase / 0.665
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.665
3kko GNPRas-related protein M-Ras / 0.665
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.664
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.664
4a1z ADPKinesin-like protein KIF11 / 0.664
1yra GDPGPN-loop GTPase PAB0955 / 0.663
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.663
4l16 ADPFidgetin-like protein 1 3.6.4 0.663
1x1r GDPRas-related protein M-Ras / 0.662
1z2c GNPRho-related GTP-binding protein RhoC / 0.662
1z6t ADPApoptotic protease-activating factor 1 / 0.662
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.662
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.662
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.662
4g01 GDPRas-related protein RABF2b / 0.662
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.661
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.661
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.660
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.660
4hdq GNPRas-related protein Rap-1b / 0.660
4iok ADPFormate--tetrahydrofolate ligase / 0.660
4mkf AP5Adenylate kinase / 0.660
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.659
4tyq AP5Adenylate kinase / 0.659
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.658
4xsg GSPTransforming protein RhoA / 0.658
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.657
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.657
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.656
3tgp GNPGTPase HRas / 0.656
4ike ADPAdenylate kinase / 0.656
2eck ADPAdenylate kinase / 0.655
3qi2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.655
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.655
1ii6 ADPKinesin-like protein KIF11 / 0.654
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.654
4ww4 ADPRuvB-like helicase / 0.654
5c46 GSPRas-related protein Rab-11A / 0.654
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.653
2l0x GDPGTP-binding protein Rheb / 0.653
4o3m ADPBloom syndrome protein 3.6.4.12 0.653
1nly AGSCag alpha / 0.652
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.651
4d0l GSPRas-related protein Rab-11A / 0.651
4jl6 ADPAdenylate kinase / 0.651
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.651
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.650
3mjh GTPRas-related protein Rab-5A / 0.650
3tnf GNPRas-related protein Rab-8A / 0.650
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.650