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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
1k6m AGS 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 1.195
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.958
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.915
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.901
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.898
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.879
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.868
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.801
1l8q ADPChromosomal replication initiator protein DnaA / 0.777
4lhv GDPRas-related protein Rab-8A / 0.770
4b7b ADPKinesin-like protein KIF11 / 0.765
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.764
2fna ADPUncharacterized protein / 0.761
2gm1 ADPKinesin-like protein KIF11 / 0.761
4jlo ADPAdenylate kinase / 0.761
2uyi ADPKinesin-like protein KIF11 / 0.753
2x2r ADPKinesin-like protein KIF11 / 0.753
3l9h ADPKinesin-like protein KIF11 / 0.752
2fl2 ADPKinesin-like protein KIF11 / 0.751
2y65 ADPKinesin heavy chain / 0.751
5dif GNPGTP-binding nuclear protein Ran / 0.751
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.750
2xae ADPKinesin-like protein KIF11 / 0.749
4ike ADPAdenylate kinase / 0.747
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.747
4qos ADPPsp operon transcriptional activator / 0.747
4zca ADPKinesin-like protein KIF11 / 0.747
3r9i ADPSeptum site-determining protein MinD / 0.745
4epx GDPGTPase KRas / 0.745
4z54 GDPNeuronal-specific septin-3 / 0.745
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.744
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.744
3ea5 GDPGTP-binding nuclear protein Ran / 0.742
4lpk GDPGTPase KRas / 0.741
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.739
5fl3 ADPPili retraction protein PilT / 0.739
1sdm ADPKinesin heavy chain-like protein / 0.737
4a1z ADPKinesin-like protein KIF11 / 0.735
1ake AP5Adenylate kinase / 0.734
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.734
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.734
2q2z ADPKinesin-like protein KIF11 / 0.733
3kkq GDPRas-related protein M-Ras / 0.733
4hse ADPChaperone protein ClpB / 0.733
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.732
4asu ADPATP synthase subunit alpha, mitochondrial / 0.731
3tlx ADPAdenylate kinase 2 / 0.730
4gp6 ADPMetallophosphoesterase / 0.730
2zrj AGSProtein RecA / 0.729
4hi0 GDPUrease accessory protein UreG / 0.729
4o2l GTPGTP-binding protein Rheb / 0.729
5aun ADPIron-sulfur cluster carrier protein / 0.729
1sq5 ADPPantothenate kinase 2.7.1.33 0.728
1yrs ADPKinesin-like protein KIF11 / 0.728
1jx2 ADPMyosin-2 heavy chain / 0.727
2r9v ATPATP synthase subunit alpha / 0.727
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.727
1d5c GDPGTPase (Rab6) / 0.726
1wbb ADPDNA mismatch repair protein MutS / 0.726
1z0d GDPRas-related protein Rab-5C / 0.726
3q5d GDPAtlastin-1 3.6.5 0.726
4uj3 GNPRas-related protein Rab-11A / 0.726
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.726
2bku GTPGTP-binding nuclear protein Ran / 0.725
2xsz ATPRuvB-like 2 3.6.4.12 0.724
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.723
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.723
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.720
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.719
3pcr GTPADP-ribosylation factor 6 / 0.719
3tqc ADPPantothenate kinase / 0.719
2vos ADPFolylpolyglutamate synthase / 0.718
4pjk ADPMyosin-2 heavy chain / 0.718
4a51 ADPKinesin-like protein KIF11 / 0.717
4jl6 ADPAdenylate kinase / 0.717
4epw GDPGTPase KRas / 0.716
4yqf GDPSeptin-9 / 0.716
1g16 GDPRas-related protein SEC4 / 0.715
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.715
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.715
3ftq GNPSeptin-2 / 0.715
4dsu GDPGTPase KRas / 0.715
4pk4 ADPUnconventional myosin-VI / 0.714
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.714
5ftc ADPTPR domain protein / 0.714
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.712
2pg2 ADPKinesin-like protein KIF11 / 0.712
3kud GDPGTPase HRas / 0.712
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.712
3a6p GTPGTP-binding nuclear protein Ran / 0.711
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.710
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.709
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.709
2ce2 GDPGTPase HRas / 0.708
3vhx GTPADP-ribosylation factor 6 / 0.708
3myk ANPMyosin-2 heavy chain / 0.707
4ldj GDPGTPase KRas / 0.707
3mjh GTPRas-related protein Rab-5A / 0.706
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.706
4luc GDPGTPase KRas / 0.706
4pfp ADPUnconventional myosin-VI / 0.706
4l8g GDPGTPase KRas / 0.705
2zfi ADPKinesin-like protein KIF1A / 0.704
4l9s GDPGTPase HRas / 0.704
4ww4 ADPRuvB-like helicase / 0.704
3cph GDPRas-related protein SEC4 / 0.703
3zfd ANPChromosome-associated kinesin KIF4 / 0.703
4obe GDPGTPase KRas / 0.703
2c5l GTPGTPase HRas / 0.701
4o2r GDPGTP-binding protein Rheb / 0.701
4q03 GDPGTPase KRas / 0.701
4ql3 GDPGTPase KRas / 0.701
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.700
3x1w GDPRas-related protein Rap-1b / 0.700
4q02 GDPGTPase KRas / 0.700
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.700
3l1c ADPProtein claret segregational / 0.699
4db1 ANPMyosin-7 / 0.699
2zts ADPUncharacterized protein / 0.698
4dso GSPGTPase KRas / 0.698
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.697
2fe4 GDPRas-related protein Rab-6B / 0.697
4ncl GDPEukaryotic translation initiation factor 5B / 0.697
2cl6 CAGGTPase HRas / 0.696
1am4 GNPCell division control protein 42 homolog / 0.695
1x1r GDPRas-related protein M-Ras / 0.695
1yra GDPGPN-loop GTPase PAB0955 / 0.695
2x7e ADPKinesin-like protein KIF11 / 0.694
3tjz GNPADP-ribosylation factor 1 / 0.694
3zia ATPATP synthase subunit alpha, mitochondrial / 0.694
4d81 ADPAAA ATPase, central domain protein / 0.694
4jjz ADPFormate--tetrahydrofolate ligase / 0.694
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.693
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.692
1wdt GTPElongation factor G (EF-G-2) / 0.692
3t1t GDPProbable gliding protein mglA / 0.692
4nh0 ATPESX secretion system protein EccC / 0.692
2qen ADPWalker-Type ATPase / 0.691
3thy ADPDNA mismatch repair protein Msh2 / 0.691
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.690
4lrw GDPGTPase KRas / 0.690
4qbi AP5Adenylate kinase / 0.690
5jlj GNPGTP-binding nuclear protein Ran / 0.690
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.689
2dr3 ADPUPF0273 protein PH0284 / 0.688
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.688
5cyo GDPSeptin-9 / 0.688
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.687
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.687
1xmv ADPProtein RecA / 0.687
1z2c GNPRho-related GTP-binding protein RhoC / 0.687
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.687
3kuc GDPRas-related protein Rap-1A / 0.685
4ap0 ADPKinesin-like protein KIF11 / 0.685
4jl5 ADPAdenylate kinase / 0.685
2g1q ADPKinesin-like protein KIF11 / 0.684
2hld ANPATP synthase subunit alpha, mitochondrial / 0.684
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
4wa7 GDPGTPase KRas / 0.683
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.682
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.681
4pjj ADPUnconventional myosin-VI / 0.681
4y0v GDPADP-ribosylation factor 1, putative / 0.681
4ylg GDPADP-ribosylation factor 1, putative / 0.681
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.680
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.680
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.680
1z0a GDPRas-related protein Rab-2A / 0.680
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.680
4lhw GNPRas-related protein Rab-8A / 0.680
3ea0 ATPATPase, ParA family / 0.679
4a28 ADPKinesin-like protein KIF11 / 0.679
4iok ADPFormate--tetrahydrofolate ligase / 0.679
4qxa GTPRas-related protein Rab-9A / 0.679
1b7t ADPMyosin heavy chain, striated muscle / 0.678
3b1x GNPFerrous iron transport protein B / 0.678
4hdq GNPRas-related protein Rap-1b / 0.678
4rkf GNPRas-related protein Rab-3 / 0.678
1sxj ADPReplication factor C subunit 5 / 0.677
4oi2 ADPProtein clpf-1 / 0.677
1tu3 GNPRas-related protein Rab-5A / 0.676
1yu9 GNPRas-related protein Rab-4A / 0.676
4idn GNPAtlastin-1 3.6.5 0.676
1ny5 ADPTranscriptional regulator (NtrC family) / 0.675
1ky2 GNPGTP-binding protein YPT7 / 0.674
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.674
1w7i ADPUnconventional myosin-Va / 0.674
4g0n GNPGTPase HRas / 0.673
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.672
1ibr GNPGTP-binding nuclear protein Ran / 0.671
4xvq GNPGTPase HRas / 0.671
1zc3 GNPRas-related protein Ral-A / 0.670
2vor ACPFolylpolyglutamate synthase / 0.670
3d8b ADPFidgetin-like protein 1 3.6.4 0.670
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.670
4dlt GNPGTPase HRas / 0.670
5d3q GDPDynamin-1 3.6.5.5 0.670
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.669
3nbx ADPATPase RavA 3.6.3 0.669
3rsl GNPGTPase HRas / 0.669
1mma ADPMyosin-2 heavy chain / 0.668
3lbn GNPGTPase HRas / 0.668
3rs0 GNPGTPase HRas / 0.668
4cf7 ADPAdenylate kinase / 0.668
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.667
3oiv GNPGTPase HRas / 0.667
4cym GCPRas-related protein Rab-32 / 0.667
4xvr GNPGTPase HRas / 0.667
1mab ATPATP synthase subunit alpha, mitochondrial / 0.666
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.666
1rrg GDPADP-ribosylation factor 1 / 0.666
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.665
3ddc GNPGTPase HRas / 0.665
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.664
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.664
3x1z GNPRas-related protein Rap-1b / 0.664
4jld ADPAdenylate kinase / 0.664
1k5d GNPGTP-binding nuclear protein Ran / 0.663
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.663
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.663
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.663
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.662
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
3tso GNPRas-related protein Rab-25 / 0.662
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.661
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.661
4uj5 GNPRas-related protein Rab-11A / 0.661
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.660
3law GNPRas-related protein Rab-7a / 0.660
1yzq GNPRas-related protein Rab-6A / 0.659
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.659
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.659
4tq9 GDPGTPase KRas / 0.659
3a58 GNPGTP-binding protein RHO1 / 0.658
4js0 GNPCell division control protein 42 homolog / 0.658
5bn3 ADPV-type ATP synthase alpha chain / 0.658
5bn3 ADPNEQ263 / 0.658
1zc4 GNPRas-related protein Ral-A / 0.657
2bbw GP5Adenylate kinase 4, mitochondrial / 0.657
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.657
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.655
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.654
3oiw GNPGTPase HRas / 0.654
4dlz GNPGTPase HRas / 0.654
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.653
3rs5 GNPGTPase HRas / 0.653
1nly AGSCag alpha / 0.652
3q9l ATPSeptum site-determining protein MinD / 0.652
3qt6 2P0Mevalonate diphosphate decarboxylase / 0.652
1p9w ANPType II secretion system protein E / 0.651
5bn4 ANPV-type ATP synthase alpha chain / 0.651
5dha GNPGTP-binding nuclear protein Ran / 0.651
2c98 ADPPsp operon transcriptional activator / 0.650
2o8b ADPDNA mismatch repair protein Msh2 / 0.650
3bxz ADPProtein translocase subunit SecA / 0.650
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.650