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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
2ax4 ADP Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.913
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.842
3ea5 GDPGTP-binding nuclear protein Ran / 0.789
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.782
4cf7 ADPAdenylate kinase / 0.748
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.743
1xmv ADPProtein RecA / 0.735
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.735
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.730
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.729
2zts ADPUncharacterized protein / 0.729
3t1t GDPProbable gliding protein mglA / 0.729
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.727
3qbv GDPCell division control protein 42 homolog / 0.726
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.725
3d8b ADPFidgetin-like protein 1 3.6.4 0.724
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.723
4jl6 ADPAdenylate kinase / 0.721
3cph GDPRas-related protein SEC4 / 0.720
4jlo ADPAdenylate kinase / 0.720
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.719
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.719
2xae ADPKinesin-like protein KIF11 / 0.719
2zfi ADPKinesin-like protein KIF1A / 0.719
3tqc ADPPantothenate kinase / 0.719
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.718
3ieu GDPGTPase Era / 0.718
1wbb ADPDNA mismatch repair protein MutS / 0.717
2bku GTPGTP-binding nuclear protein Ran / 0.717
4q03 GDPGTPase KRas / 0.716
1jx2 ADPMyosin-2 heavy chain / 0.715
2x2r ADPKinesin-like protein KIF11 / 0.715
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.714
2fna ADPUncharacterized protein / 0.714
4a28 ADPKinesin-like protein KIF11 / 0.712
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.712
4pfp ADPUnconventional myosin-VI / 0.712
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.711
1mma ADPMyosin-2 heavy chain / 0.710
4hse ADPChaperone protein ClpB / 0.710
4qbg AP5Adenylate kinase / 0.710
4pjk ADPMyosin-2 heavy chain / 0.709
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.709
4l8g GDPGTPase KRas / 0.708
4pk4 ADPUnconventional myosin-VI / 0.708
4y0v GDPADP-ribosylation factor 1, putative / 0.708
4ylg GDPADP-ribosylation factor 1, putative / 0.708
1d5c GDPGTPase (Rab6) / 0.706
1g16 GDPRas-related protein SEC4 / 0.706
1sdm ADPKinesin heavy chain-like protein / 0.706
1z0f GDPRas-related protein Rab-14 / 0.706
3mjh GTPRas-related protein Rab-5A / 0.706
4epw GDPGTPase KRas / 0.706
5cyo GDPSeptin-9 / 0.706
4l9s GDPGTPase HRas / 0.705
4o2r GDPGTP-binding protein Rheb / 0.705
3kkq GDPRas-related protein M-Ras / 0.704
3l9h ADPKinesin-like protein KIF11 / 0.704
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.704
4obe GDPGTPase KRas / 0.704
5fl3 ADPPili retraction protein PilT / 0.704
3kuc GDPRas-related protein Rap-1A / 0.703
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.702
4wa7 GDPGTPase KRas / 0.702
1mmg AGSMyosin-2 heavy chain / 0.701
3cob ADPKinesin heavy chain-like protein / 0.701
4lrw GDPGTPase KRas / 0.701
4lv6 GDPGTPase KRas / 0.701
4q02 GDPGTPase KRas / 0.701
4tq9 GDPGTPase KRas / 0.701
1x1r GDPRas-related protein M-Ras / 0.700
2uyi ADPKinesin-like protein KIF11 / 0.700
4dsu GDPGTPase KRas / 0.700
5bn3 ADPV-type ATP synthase alpha chain / 0.700
5bn3 ADPNEQ263 / 0.700
4b7b ADPKinesin-like protein KIF11 / 0.698
4epx GDPGTPase KRas / 0.698
2zro ADPProtein RecA / 0.697
4pjj ADPUnconventional myosin-VI / 0.697
2dpx GDPGTP-binding protein RAD / 0.696
2gm1 ADPKinesin-like protein KIF11 / 0.696
3x1w GDPRas-related protein Rap-1b / 0.696
1sq5 ADPPantothenate kinase 2.7.1.33 0.695
1yrs ADPKinesin-like protein KIF11 / 0.695
3r9i ADPSeptum site-determining protein MinD / 0.695
4d0l GSPRas-related protein Rab-11A / 0.695
1ow3 GDPTransforming protein RhoA / 0.694
1yra GDPGPN-loop GTPase PAB0955 / 0.694
2fe4 GDPRas-related protein Rab-6B / 0.693
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.693
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.692
3wyf GTPGTP-binding nuclear protein / 0.692
4xsg GSPTransforming protein RhoA / 0.692
4asu ADPATP synthase subunit alpha, mitochondrial / 0.691
4hi0 GDPUrease accessory protein UreG / 0.691
4xoi GTPTransforming protein RhoA / 0.691
1rrg GDPADP-ribosylation factor 1 / 0.690
3tjz GNPADP-ribosylation factor 1 / 0.690
4g01 GDPRas-related protein RABF2b / 0.690
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.689
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.689
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
2zrj AGSProtein RecA / 0.689
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.688
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.688
4iok ADPFormate--tetrahydrofolate ligase / 0.688
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.687
1m7b GTPRho-related GTP-binding protein RhoE / 0.686
3qi2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.686
4ap0 ADPKinesin-like protein KIF11 / 0.686
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.685
1z2a GDPRas-related protein Rab-23 / 0.685
2pg2 ADPKinesin-like protein KIF11 / 0.685
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.685
4zca ADPKinesin-like protein KIF11 / 0.685
5aun ADPIron-sulfur cluster carrier protein / 0.685
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.684
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.684
4k81 GTPGTPase HRas / 0.684
1wdt GTPElongation factor G (EF-G-2) / 0.683
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.683
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.683
4yqf GDPSeptin-9 / 0.683
1n6m ADPProtein claret segregational / 0.682
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.682
4a1z ADPKinesin-like protein KIF11 / 0.682
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.681
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.681
4gp6 ADPMetallophosphoesterase / 0.680
3bbp GTPRas-related protein Rab-6A / 0.678
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.678
1t91 GTPRas-related protein Rab-7a / 0.677
1wa5 GTPGTP-binding nuclear protein Ran / 0.677
5d3q GDPDynamin-1 3.6.5.5 0.677
2fl2 ADPKinesin-like protein KIF11 / 0.676
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.676
2vf7 ADPUvrABC system protein A / 0.675
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.675
4lhv GDPRas-related protein Rab-8A / 0.674
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.673
4jky ADPAdenylate kinase / 0.673
4ncl GDPEukaryotic translation initiation factor 5B / 0.673
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.672
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
1yu9 GNPRas-related protein Rab-4A / 0.672
2g1q ADPKinesin-like protein KIF11 / 0.672
3oiu GNPGTPase HRas / 0.672
2eck ADPAdenylate kinase / 0.671
3ref GDPRho family GTPase / 0.671
1g6o ADPCag alpha / 0.670
1s3g AP5Adenylate kinase / 0.670
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.670
3oiw GNPGTPase HRas / 0.670
2zr9 DTPProtein RecA / 0.669
4dso GSPGTPase KRas / 0.669
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.669
1oix GDPRas-related protein Rab-11A / 0.667
2ce2 GDPGTPase HRas / 0.667
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.667
2o8b ADPDNA mismatch repair protein Msh2 / 0.667
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.667
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.667
4d81 ADPAAA ATPase, central domain protein / 0.667
5ftc ADPTPR domain protein / 0.667
1z0d GDPRas-related protein Rab-5C / 0.666
4dxa GSPRas-related protein Rap-1b / 0.666
2zet GTPRas-related protein Rab-27B / 0.665
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.665
4a51 ADPKinesin-like protein KIF11 / 0.665
1b7t ADPMyosin heavy chain, striated muscle / 0.664
2x7e ADPKinesin-like protein KIF11 / 0.664
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.664
3i3s GNPGTPase HRas / 0.664
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.664
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.663
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.663
4lj7 MNTChaperone protein ClpB / 0.663
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.662
3b1x GNPFerrous iron transport protein B / 0.662
4lhw GNPRas-related protein Rab-8A / 0.662
5dha GNPGTP-binding nuclear protein Ran / 0.662
5hpy GDPTransforming protein RhoA / 0.662
1ky2 GNPGTP-binding protein YPT7 / 0.661
2bbw GP5Adenylate kinase 4, mitochondrial / 0.660
2j7p GNPSignal recognition particle protein / 0.660
2j7p GNPSignal recognition particle receptor FtsY / 0.660
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.660
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.660
4mkh AP5Adenylate kinase / 0.660
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.659
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.659
2c9o ADPRuvB-like 1 3.6.4.12 0.659
3tgp GNPGTPase HRas / 0.659
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.658
1f5n GNPGuanylate-binding protein 1 / 0.658
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.658
1tu3 GNPRas-related protein Rab-5A / 0.658
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.658
4ike ADPAdenylate kinase / 0.658
4jld ADPAdenylate kinase / 0.658
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.657
4rkf GNPRas-related protein Rab-3 / 0.657
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.656
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.656
3kud GDPGTPase HRas / 0.656
5da9 AGSUncharacterized protein / 0.656
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.655
3bc1 GNPRas-related protein Rab-27A / 0.655
4jl5 ADPAdenylate kinase / 0.655
4xvu ATPATPase GET3 / 0.655
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.655
1cxz GSPTransforming protein RhoA / 0.654
2q3f GNPRas-related GTP-binding protein D / 0.654
3dzd ADPTranscriptional regulator (NtrC family) / 0.654
3nbz GTPGTP-binding nuclear protein Ran / 0.654
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.653
1n6l GTPRas-related protein Rab-5A / 0.653
2ql6 ADPNicotinamide riboside kinase 1 / 0.653
2r9v ATPATP synthase subunit alpha / 0.653
3k9l GNPGTPase HRas / 0.653
1xtr GNPGTP-binding protein Rheb / 0.652
1z6t ADPApoptotic protease-activating factor 1 / 0.652
2bme GNPRas-related protein Rab-4A / 0.652
3oes GNPGTPase RhebL1 / 0.652
4goj GNPADP-ribosylation factor-like protein 3 / 0.652
4i1v ADPDephospho-CoA kinase / 0.652
4jjz ADPFormate--tetrahydrofolate ligase / 0.652
4luc GDPGTPase KRas / 0.652
4uj3 GNPRas-related protein Rab-11A / 0.652
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.651
1am4 GNPCell division control protein 42 homolog / 0.650
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.650