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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
2i1v ADP 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 1.087
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 1.039
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 1.015
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.994
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.985
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.915
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.870
4z54 GDPNeuronal-specific septin-3 / 0.799
3q5d GDPAtlastin-1 3.6.5 0.782
2x2r ADPKinesin-like protein KIF11 / 0.780
2uyi ADPKinesin-like protein KIF11 / 0.779
2pg2 ADPKinesin-like protein KIF11 / 0.778
2xae ADPKinesin-like protein KIF11 / 0.775
3cob ADPKinesin heavy chain-like protein / 0.773
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.770
2y65 ADPKinesin heavy chain / 0.765
3tqc ADPPantothenate kinase / 0.765
4b7b ADPKinesin-like protein KIF11 / 0.765
4qbh AP5Adenylate kinase / 0.764
1sq5 ADPPantothenate kinase 2.7.1.33 0.762
2zfi ADPKinesin-like protein KIF1A / 0.762
1sdm ADPKinesin heavy chain-like protein / 0.760
2zts ADPUncharacterized protein / 0.760
2fna ADPUncharacterized protein / 0.759
4a1z ADPKinesin-like protein KIF11 / 0.758
5cyo GDPSeptin-9 / 0.757
4lrw GDPGTPase KRas / 0.756
3qbv GDPCell division control protein 42 homolog / 0.755
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.754
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.749
3cph GDPRas-related protein SEC4 / 0.748
4zca ADPKinesin-like protein KIF11 / 0.748
3kkq GDPRas-related protein M-Ras / 0.745
2zrj AGSProtein RecA / 0.744
1b7t ADPMyosin heavy chain, striated muscle / 0.742
2x7e ADPKinesin-like protein KIF11 / 0.742
3l1c ADPProtein claret segregational / 0.742
1z0a GDPRas-related protein Rab-2A / 0.741
1x1r GDPRas-related protein M-Ras / 0.740
2fl2 ADPKinesin-like protein KIF11 / 0.740
4asu ADPATP synthase subunit alpha, mitochondrial / 0.740
3ea5 GDPGTP-binding nuclear protein Ran / 0.739
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.739
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.738
1nly AGSCag alpha / 0.737
1wbb ADPDNA mismatch repair protein MutS / 0.737
4dzz ADPPlasmid partitioning protein ParF / 0.737
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.736
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.736
4hi0 GDPUrease accessory protein UreG / 0.735
4idp GNPAtlastin-1 3.6.5 0.735
5fl3 ADPPili retraction protein PilT / 0.735
3t1t GDPProbable gliding protein mglA / 0.734
3l9h ADPKinesin-like protein KIF11 / 0.732
4qxa GTPRas-related protein Rab-9A / 0.732
4qm6 GTPMetallophosphoesterase / 0.731
4a28 ADPKinesin-like protein KIF11 / 0.730
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.729
5bn3 ADPV-type ATP synthase alpha chain / 0.729
5bn3 ADPNEQ263 / 0.729
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.728
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.726
4obe GDPGTPase KRas / 0.726
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.726
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.725
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.725
4ihq ADPConserved Archaeal protein / 0.725
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.725
4ap0 ADPKinesin-like protein KIF11 / 0.724
1mmg AGSMyosin-2 heavy chain / 0.723
4tq9 GDPGTPase KRas / 0.723
3pcr GTPADP-ribosylation factor 6 / 0.722
4q02 GDPGTPase KRas / 0.722
4yqf GDPSeptin-9 / 0.722
4lhv GDPRas-related protein Rab-8A / 0.721
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.720
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.718
2gcp GSPRho-related GTP-binding protein RhoC / 0.718
3kud GDPGTPase HRas / 0.718
4wa7 GDPGTPase KRas / 0.718
4x8o AP5Adenylate kinase / 0.718
4a51 ADPKinesin-like protein KIF11 / 0.717
1ii6 ADPKinesin-like protein KIF11 / 0.716
1mma ADPMyosin-2 heavy chain / 0.716
1f5n GNPGuanylate-binding protein 1 / 0.715
2l0x GDPGTP-binding protein Rheb / 0.715
1oix GDPRas-related protein Rab-11A / 0.714
1z0f GDPRas-related protein Rab-14 / 0.714
4l8g GDPGTPase KRas / 0.713
4ncl GDPEukaryotic translation initiation factor 5B / 0.713
3zfd ANPChromosome-associated kinesin KIF4 / 0.712
4l9s GDPGTPase HRas / 0.712
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.711
1sxj ADPReplication factor C subunit 5 / 0.710
4epw GDPGTPase KRas / 0.710
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.709
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.709
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.709
3x1w GDPRas-related protein Rap-1b / 0.709
4gp6 ADPMetallophosphoesterase / 0.709
5ftc ADPTPR domain protein / 0.709
2fe4 GDPRas-related protein Rab-6B / 0.708
4iok ADPFormate--tetrahydrofolate ligase / 0.708
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.708
5aun ADPIron-sulfur cluster carrier protein / 0.708
1l8q ADPChromosomal replication initiator protein DnaA / 0.706
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.706
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.704
1z2a GDPRas-related protein Rab-23 / 0.704
1g16 GDPRas-related protein SEC4 / 0.703
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.703
2q2z ADPKinesin-like protein KIF11 / 0.703
4hse ADPChaperone protein ClpB / 0.703
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.703
1ank ANPAdenylate kinase / 0.702
1rrg GDPADP-ribosylation factor 1 / 0.702
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.702
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.701
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.700
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.700
1wdt GTPElongation factor G (EF-G-2) / 0.700
2bme GNPRas-related protein Rab-4A / 0.700
4nh0 ATPESX secretion system protein EccC / 0.700
4oi2 ADPProtein clpf-1 / 0.700
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.699
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.699
2dr3 ADPUPF0273 protein PH0284 / 0.699
4k81 GTPGTPase HRas / 0.699
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.699
2ce2 GDPGTPase HRas / 0.698
4xvu ATPATPase GET3 / 0.698
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.697
3tgp GNPGTPase HRas / 0.697
4o3m ADPBloom syndrome protein 3.6.4.12 0.697
1yrs ADPKinesin-like protein KIF11 / 0.695
4db1 ANPMyosin-7 / 0.695
2zro ADPProtein RecA / 0.694
3bxz ADPProtein translocase subunit SecA / 0.694
3nbx ADPATPase RavA 3.6.3 0.693
3zia ATPATP synthase subunit alpha, mitochondrial / 0.693
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.693
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.692
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.692
2gil GTPRas-related protein Rab-6A / 0.692
3thy ADPDNA mismatch repair protein Msh2 / 0.692
2ncd ADPProtein claret segregational / 0.691
2o8b ADPDNA mismatch repair protein Msh2 / 0.691
3c41 ANPAmino acid ABC transporter / 0.691
4luc GDPGTPase KRas / 0.691
1zbd GTPRas-related protein Rab-3A / 0.690
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.690
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.690
4o2r GDPGTP-binding protein Rheb / 0.690
1yra GDPGPN-loop GTPase PAB0955 / 0.688
3hpq AP5Adenylate kinase / 0.688
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.687
4idn GNPAtlastin-1 3.6.5 0.687
1ow3 GDPTransforming protein RhoA / 0.686
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.686
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.686
4hdq GNPRas-related protein Rap-1b / 0.686
4o25 GTPGTP-binding protein Rheb / 0.686
1uad GNPRas-related protein Ral-A / 0.685
1xp8 AGSProtein RecA / 0.685
2g1q ADPKinesin-like protein KIF11 / 0.685
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.685
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.685
4lpk GDPGTPase KRas / 0.685
4xvr GNPGTPase HRas / 0.685
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.684
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.684
3ftq GNPSeptin-2 / 0.684
3k9l GNPGTPase HRas / 0.684
1g6o ADPCag alpha / 0.682
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.682
1lfd GNPGTPase HRas / 0.682
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.682
2rgg GNPGTPase HRas / 0.682
4lv6 GDPGTPase KRas / 0.682
1fnn ADPORC1-type DNA replication protein / 0.678
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.677
1ky2 GNPGTP-binding protein YPT7 / 0.677
3mjh GTPRas-related protein Rab-5A / 0.677
1v8k ANPKinesin-like protein KIF2C / 0.676
2xto GDPGTPase IMAP family member 2 / 0.676
4ldj GDPGTPase KRas / 0.676
4q03 GDPGTPase KRas / 0.675
4ql3 GDPGTPase KRas / 0.675
3myk ANPMyosin-2 heavy chain / 0.674
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.673
4e07 ACPPlasmid partitioning protein ParF / 0.673
4epx GDPGTPase KRas / 0.673
2vp4 DCPDeoxynucleoside kinase / 0.672
4kod ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.672
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.671
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.671
1n6m ADPProtein claret segregational / 0.669
3law GNPRas-related protein Rab-7a / 0.669
4dsu GDPGTPase KRas / 0.669
1svw GTPProbable GTP-binding protein EngB / 0.668
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.668
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.667
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.667
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.667
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.667
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.667
2bc9 GNPGuanylate-binding protein 1 / 0.666
1d5c GDPGTPase (Rab6) / 0.665
1jx2 ADPMyosin-2 heavy chain / 0.665
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.665
3k3b ADPKinesin-like protein KIF11 / 0.665
4ohx ADPProtein clpf-1 / 0.665
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.664
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.664
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.663
2gbl ATPCircadian clock protein kinase KaiC 2.7.11.1 0.663
4pfp ADPUnconventional myosin-VI / 0.663
2q3f GNPRas-related GTP-binding protein D / 0.662
3cf0 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.661
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.661
2fg5 GNPRas-related protein Rab-31 / 0.660
4fvq ATPTyrosine-protein kinase JAK2 / 0.660
5c46 GSPRas-related protein Rab-11A / 0.659
1am4 GNPCell division control protein 42 homolog / 0.658
1ja1 NAPNADPH--cytochrome P450 reductase / 0.658
3tjz GNPADP-ribosylation factor 1 / 0.658
4x8l AP5Adenylate kinase / 0.658
1p9w ANPType II secretion system protein E / 0.657
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.657
3b03 VNRIsopentenyl-diphosphate delta-isomerase / 0.656
4pjj ADPUnconventional myosin-VI / 0.656
4qos ADPPsp operon transcriptional activator / 0.656
1p3j AP5Adenylate kinase / 0.655
2whx ADPGenome polyprotein 3.4.21.91 0.655
3ddc GNPGTPase HRas / 0.655
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.655
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.655
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.654
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.654
4kvg GTPRas-related protein Rap-1A / 0.654
1dap NDPMeso-diaminopimelate D-dehydrogenase 1.4.1.16 0.653
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.653
2qen ADPWalker-Type ATPase / 0.653
3oiv GNPGTPase HRas / 0.653
2zsa ADPPantothenate kinase 2.7.1.33 0.652
1xms ANPProtein RecA / 0.651
3vtk ADPThymidine kinase / 0.651
4iei ADPGene 2 protein / 0.651
5cyp GSPSeptin-9 / 0.651
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.650
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650