Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
1bif AGS 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 1.195
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.958
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.897
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.884
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.870
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.870
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.864
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.814
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.794
4z54 GDPNeuronal-specific septin-3 / 0.772
4pjj ADPUnconventional myosin-VI / 0.769
2eck ADPAdenylate kinase / 0.767
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.765
3tqc ADPPantothenate kinase / 0.762
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.758
3k1j ADPATP-dependent protease Lon / 0.758
1jx2 ADPMyosin-2 heavy chain / 0.756
1mmg AGSMyosin-2 heavy chain / 0.756
4jsy GTPMetallophosphoesterase / 0.756
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.755
1sq5 ADPPantothenate kinase 2.7.1.33 0.755
3l9h ADPKinesin-like protein KIF11 / 0.753
4yqf GDPSeptin-9 / 0.753
4b7b ADPKinesin-like protein KIF11 / 0.752
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.752
4lhv GDPRas-related protein Rab-8A / 0.751
1mma ADPMyosin-2 heavy chain / 0.750
4idn GNPAtlastin-1 3.6.5 0.750
1xmv ADPProtein RecA / 0.749
4dsu GDPGTPase KRas / 0.748
2zrj AGSProtein RecA / 0.747
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.746
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.746
4c2u ANPDNA helicase / 0.746
4lrw GDPGTPase KRas / 0.746
2xsz ATPRuvB-like 2 3.6.4.12 0.745
3cob ADPKinesin heavy chain-like protein / 0.745
4epx GDPGTPase KRas / 0.745
4db1 ANPMyosin-7 / 0.744
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.742
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.741
3tgp GNPGTPase HRas / 0.741
3x1z GNPRas-related protein Rap-1b / 0.741
5cyo GDPSeptin-9 / 0.741
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.739
2x7e ADPKinesin-like protein KIF11 / 0.739
3oes GNPGTPase RhebL1 / 0.739
4uj5 GNPRas-related protein Rab-11A / 0.737
1b7t ADPMyosin heavy chain, striated muscle / 0.736
1fmw ATPMyosin-2 heavy chain / 0.736
4q03 GDPGTPase KRas / 0.736
2c5l GTPGTPase HRas / 0.735
2zts ADPUncharacterized protein / 0.735
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.735
4pk4 ADPUnconventional myosin-VI / 0.735
4ql3 GDPGTPase KRas / 0.735
3vhx GTPADP-ribosylation factor 6 / 0.734
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.734
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.733
1z2a GDPRas-related protein Rab-23 / 0.733
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.733
4a51 ADPKinesin-like protein KIF11 / 0.732
4ldj GDPGTPase KRas / 0.732
3kud GDPGTPase HRas / 0.731
3zfd ANPChromosome-associated kinesin KIF4 / 0.731
4luc GDPGTPase KRas / 0.731
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.731
4tq9 GDPGTPase KRas / 0.731
1oix GDPRas-related protein Rab-11A / 0.730
1wdt GTPElongation factor G (EF-G-2) / 0.730
3nbx ADPATPase RavA 3.6.3 0.730
2ce2 GDPGTPase HRas / 0.729
3wyf GTPGTP-binding nuclear protein / 0.729
3x1w GDPRas-related protein Rap-1b / 0.729
4wa7 GDPGTPase KRas / 0.729
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.728
4epw GDPGTPase KRas / 0.728
1z0a GDPRas-related protein Rab-2A / 0.727
4o2l GTPGTP-binding protein Rheb / 0.727
4q02 GDPGTPase KRas / 0.727
4zca ADPKinesin-like protein KIF11 / 0.727
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.726
3mjh GTPRas-related protein Rab-5A / 0.726
1ake AP5Adenylate kinase / 0.725
2bc9 GNPGuanylate-binding protein 1 / 0.725
4o2r GDPGTP-binding protein Rheb / 0.725
2fe4 GDPRas-related protein Rab-6B / 0.724
3kz1 GSPTransforming protein RhoA / 0.724
1d5c GDPGTPase (Rab6) / 0.723
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.722
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.722
3a6p GTPGTP-binding nuclear protein Ran / 0.722
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.722
3m0e ATPTranscriptional regulator (NtrC family) / 0.722
3tjz GNPADP-ribosylation factor 1 / 0.722
4d0l GSPRas-related protein Rab-11A / 0.722
2uyi ADPKinesin-like protein KIF11 / 0.721
3uk6 ADPRuvB-like 2 3.6.4.12 0.721
2c96 ATPPsp operon transcriptional activator / 0.720
2j5x GSPADP-ribosylation factor 6 / 0.720
4itr GDPCell division control protein 42 homolog / 0.719
3pcr GTPADP-ribosylation factor 6 / 0.717
4ncl GDPEukaryotic translation initiation factor 5B / 0.716
3ref GDPRho family GTPase / 0.715
3zia ATPATP synthase subunit alpha, mitochondrial / 0.715
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.715
4uj3 GNPRas-related protein Rab-11A / 0.715
1g16 GDPRas-related protein SEC4 / 0.714
1yrs ADPKinesin-like protein KIF11 / 0.714
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.714
2dpx GDPGTP-binding protein RAD / 0.714
3q5d GDPAtlastin-1 3.6.5 0.714
4dso GSPGTPase KRas / 0.714
4jld ADPAdenylate kinase / 0.714
4a1z ADPKinesin-like protein KIF11 / 0.713
2ffq GSPRas-related protein Rab-6B / 0.712
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.712
4hi0 GDPUrease accessory protein UreG / 0.712
1yu9 GNPRas-related protein Rab-4A / 0.711
3c41 ANPAmino acid ABC transporter / 0.711
5k5z ANPUncharacterized protein / 0.711
2fl2 ADPKinesin-like protein KIF11 / 0.710
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.710
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.709
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.709
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.709
1am4 GNPCell division control protein 42 homolog / 0.708
1yra GDPGPN-loop GTPase PAB0955 / 0.708
4idp GNPAtlastin-1 3.6.5 0.708
4xvq GNPGTPase HRas / 0.708
1svw GTPProbable GTP-binding protein EngB / 0.706
4nh0 ATPESX secretion system protein EccC / 0.706
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.705
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.705
1tu3 GNPRas-related protein Rab-5A / 0.704
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.704
4lpk GDPGTPase KRas / 0.704
1n6l GTPRas-related protein Rab-5A / 0.703
1svm ATPLarge T antigen 3.6.4 0.702
4goj GNPADP-ribosylation factor-like protein 3 / 0.702
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.701
2ncd ADPProtein claret segregational / 0.701
4qos ADPPsp operon transcriptional activator / 0.700
2cl6 CAGGTPase HRas / 0.699
2zfi ADPKinesin-like protein KIF1A / 0.699
3ddc GNPGTPase HRas / 0.699
4dlt GNPGTPase HRas / 0.699
2hld ANPATP synthase subunit alpha, mitochondrial / 0.698
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.698
3i3s GNPGTPase HRas / 0.698
3l8y GNPGTPase HRas / 0.698
3oiu GNPGTPase HRas / 0.698
3rs4 GNPGTPase HRas / 0.698
3rs5 GNPGTPase HRas / 0.698
4jjz ADPFormate--tetrahydrofolate ligase / 0.698
4tv9 GTPTubulin alpha-1B chain / 0.698
1uad GNPRas-related protein Ral-A / 0.697
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.697
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.697
4mkf AP5Adenylate kinase / 0.696
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.695
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
4oi2 ADPProtein clpf-1 / 0.695
4xvr GNPGTPase HRas / 0.695
5c46 GSPRas-related protein Rab-11A / 0.695
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.694
3thy ADPDNA mismatch repair protein Msh2 / 0.694
4hdq GNPRas-related protein Rap-1b / 0.694
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.694
2vos ADPFolylpolyglutamate synthase / 0.693
3ftq GNPSeptin-2 / 0.693
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.693
4asu ADPATP synthase subunit alpha, mitochondrial / 0.693
1w5s ADPORC1-type DNA replication protein 2 / 0.692
1z2c GNPRho-related GTP-binding protein RhoC / 0.692
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.692
3ieu GDPGTPase Era / 0.692
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.691
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.691
2l0x GDPGTP-binding protein Rheb / 0.691
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.691
3rs0 GNPGTPase HRas / 0.691
4gp6 ADPMetallophosphoesterase / 0.691
4ihq ADPConserved Archaeal protein / 0.691
4to4 DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.691
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.690
2xae ADPKinesin-like protein KIF11 / 0.690
3law GNPRas-related protein Rab-7a / 0.690
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.690
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.690
5aun ADPIron-sulfur cluster carrier protein / 0.690
1z0f GDPRas-related protein Rab-14 / 0.688
2g1q ADPKinesin-like protein KIF11 / 0.688
3qbt GNPRas-related protein Rab-8A / 0.688
3qbv GDPCell division control protein 42 homolog / 0.688
5dif GNPGTP-binding nuclear protein Ran / 0.688
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.687
4y0v GDPADP-ribosylation factor 1, putative / 0.687
4ylg GDPADP-ribosylation factor 1, putative / 0.687
3k9l GNPGTPase HRas / 0.686
3t1t GDPProbable gliding protein mglA / 0.686
4a28 ADPKinesin-like protein KIF11 / 0.686
4xoi GTPTransforming protein RhoA / 0.686
3cph GDPRas-related protein SEC4 / 0.685
1wa5 GTPGTP-binding nuclear protein Ran / 0.684
1l8q ADPChromosomal replication initiator protein DnaA / 0.683
4yj2 GTPTubulin alpha-1B chain / 0.683
1lfd GNPGTPase HRas / 0.682
1zbd GTPRas-related protein Rab-3A / 0.682
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.682
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
2iut AGSDNA translocase FtsK / 0.682
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.682
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
1kmq GNPTransforming protein RhoA / 0.681
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.681
3oiv GNPGTPase HRas / 0.681
3ryh GTPTubulin alpha chain / 0.681
4lv6 GDPGTPase KRas / 0.681
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.680
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.680
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.679
2rgc GNPGTPase HRas / 0.679
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.679
3eg5 GNPCell division control protein 42 homolog / 0.679
3kko GNPRas-related protein M-Ras / 0.679
1okk GCPSignal recognition particle protein / 0.678
1okk GCPSignal recognition particle receptor FtsY / 0.678
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.678
1zc3 GNPRas-related protein Ral-A / 0.678
2bku GTPGTP-binding nuclear protein Ran / 0.678
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.677
1p9w ANPType II secretion system protein E / 0.677
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.677
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.677
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.677
4iok ADPFormate--tetrahydrofolate ligase / 0.677
5ftc ADPTPR domain protein / 0.677
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.676
3q9l ATPSeptum site-determining protein MinD / 0.676
1vg8 GNPRas-related protein Rab-7a / 0.675
5di3 GNPADP-ribosylation factor-like protein 3 / 0.675
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.674
2vf7 ADPUvrABC system protein A / 0.674
2xto GDPGTPase IMAP family member 2 / 0.674
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.674
4dzz ADPPlasmid partitioning protein ParF / 0.674
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.673
2rgx AP5Adenylate kinase / 0.673
4dxa GSPRas-related protein Rap-1b / 0.673
1zc4 GNPRas-related protein Ral-A / 0.672
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.672
2fna ADPUncharacterized protein / 0.671
3myk ANPMyosin-2 heavy chain / 0.671
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.670
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.670
1sdm ADPKinesin heavy chain-like protein / 0.670
2r9v ATPATP synthase subunit alpha / 0.670
2rgb GNPGTPase HRas / 0.670
2rge GNPGTPase HRas / 0.670
3ea5 GDPGTP-binding nuclear protein Ran / 0.670
3kkq GDPRas-related protein M-Ras / 0.670
3oee ANPATP synthase subunit alpha, mitochondrial / 0.670
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.670
4dlv GNPGTPase HRas / 0.670
2bme GNPRas-related protein Rab-4A / 0.669
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.669
2zet GTPRas-related protein Rab-27B / 0.669
4v02 ATPSite-determining protein / 0.669
3l1c ADPProtein claret segregational / 0.668
4l8g GDPGTPase KRas / 0.668
4pfp ADPUnconventional myosin-VI / 0.668
1p3j AP5Adenylate kinase / 0.667
1x1r GDPRas-related protein M-Ras / 0.667
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.667
2gm1 ADPKinesin-like protein KIF11 / 0.667
3pit GNPRas-related protein M-Ras / 0.667
5l3s GNPSignal recognition particle receptor FtsY / 0.667
2jas DTPDeoxyguanosine kinase / 0.666
4pjk ADPMyosin-2 heavy chain / 0.666
5itz GTPTubulin alpha-1B chain / 0.666
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.665
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.665
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
5jlj GNPGTP-binding nuclear protein Ran / 0.665
5jqg GTPTubulin alpha-1B chain / 0.665
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.664
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.664
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.664
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.664
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.663
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.663
4mkh AP5Adenylate kinase / 0.663
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.662
1xtr GNPGTP-binding protein Rheb / 0.662
3bbp GTPRas-related protein Rab-6A / 0.662
4xsg GSPTransforming protein RhoA / 0.662
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.661
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
1svl ADPLarge T antigen 3.6.4 0.661
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.660
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.660
3a58 GNPGTP-binding protein RHO1 / 0.659
5d3q GDPDynamin-1 3.6.5.5 0.659
2vp4 DCPDeoxynucleoside kinase / 0.658
4i1v ADPDephospho-CoA kinase / 0.658
2y65 ADPKinesin heavy chain / 0.657
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.657
5dha GNPGTP-binding nuclear protein Ran / 0.657
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.656
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.656
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.656
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.656
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.656
4obe GDPGTPase KRas / 0.655
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.654
1sxj ADPReplication factor C subunit 5 / 0.654
4ap0 ADPKinesin-like protein KIF11 / 0.654
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.653
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.653
2q2z ADPKinesin-like protein KIF11 / 0.653
3kuc GDPRas-related protein Rap-1A / 0.653
1wbb ADPDNA mismatch repair protein MutS / 0.652
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.652
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.652
3lbh GNPGTPase HRas / 0.652
4ike ADPAdenylate kinase / 0.652
4js0 GNPCell division control protein 42 homolog / 0.652
4l9s GDPGTPase HRas / 0.652
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.651
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.651
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
2qen ADPWalker-Type ATPase / 0.650
4qm6 GTPMetallophosphoesterase / 0.650
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.650