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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
4ma4 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
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 1.081
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 1.036
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 1.015
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.968
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.967
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.898
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.897
4zca ADPKinesin-like protein KIF11 / 0.784
3k1j ADPATP-dependent protease Lon / 0.782
2x2r ADPKinesin-like protein KIF11 / 0.780
2uyi ADPKinesin-like protein KIF11 / 0.779
2zts ADPUncharacterized protein / 0.779
4z54 GDPNeuronal-specific septin-3 / 0.779
3tqc ADPPantothenate kinase / 0.778
4pjj ADPUnconventional myosin-VI / 0.778
3l9h ADPKinesin-like protein KIF11 / 0.776
1sq5 ADPPantothenate kinase 2.7.1.33 0.775
4pk4 ADPUnconventional myosin-VI / 0.774
3cob ADPKinesin heavy chain-like protein / 0.770
4lrw GDPGTPase KRas / 0.768
4b7b ADPKinesin-like protein KIF11 / 0.766
2fl2 ADPKinesin-like protein KIF11 / 0.764
2y65 ADPKinesin heavy chain / 0.764
3nbx ADPATPase RavA 3.6.3 0.764
2pg2 ADPKinesin-like protein KIF11 / 0.763
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.763
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.758
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.758
4pjk ADPMyosin-2 heavy chain / 0.758
4ql3 GDPGTPase KRas / 0.758
4epx GDPGTPase KRas / 0.757
4q03 GDPGTPase KRas / 0.757
1z0a GDPRas-related protein Rab-2A / 0.756
1z2a GDPRas-related protein Rab-23 / 0.756
4ldj GDPGTPase KRas / 0.756
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.755
1sdm ADPKinesin heavy chain-like protein / 0.754
1z0f GDPRas-related protein Rab-14 / 0.754
5fl3 ADPPili retraction protein PilT / 0.754
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.751
4lpk GDPGTPase KRas / 0.751
3q5d GDPAtlastin-1 3.6.5 0.748
4l8g GDPGTPase KRas / 0.748
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.747
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.746
2vf7 ADPUvrABC system protein A / 0.746
3kud GDPGTPase HRas / 0.746
3kkq GDPRas-related protein M-Ras / 0.745
4epw GDPGTPase KRas / 0.744
4l9s GDPGTPase HRas / 0.744
4obe GDPGTPase KRas / 0.744
1b7t ADPMyosin heavy chain, striated muscle / 0.743
2x7e ADPKinesin-like protein KIF11 / 0.743
4a1z ADPKinesin-like protein KIF11 / 0.743
4lv6 GDPGTPase KRas / 0.743
4q02 GDPGTPase KRas / 0.743
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.742
4asu ADPATP synthase subunit alpha, mitochondrial / 0.742
4tq9 GDPGTPase KRas / 0.742
1x1r GDPRas-related protein M-Ras / 0.741
4o2r GDPGTP-binding protein Rheb / 0.741
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.740
5aun ADPIron-sulfur cluster carrier protein / 0.740
2dpx GDPGTP-binding protein RAD / 0.739
1d5c GDPGTPase (Rab6) / 0.738
4a51 ADPKinesin-like protein KIF11 / 0.738
4hi0 GDPUrease accessory protein UreG / 0.738
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.736
1yrs ADPKinesin-like protein KIF11 / 0.735
1mma ADPMyosin-2 heavy chain / 0.730
4x8o AP5Adenylate kinase / 0.730
2hld ANPATP synthase subunit alpha, mitochondrial / 0.727
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.727
4lhv GDPRas-related protein Rab-8A / 0.727
2q2z ADPKinesin-like protein KIF11 / 0.725
4a28 ADPKinesin-like protein KIF11 / 0.725
4jlo ADPAdenylate kinase / 0.725
3t1t GDPProbable gliding protein mglA / 0.724
3ieu GDPGTPase Era / 0.723
3uk6 ADPRuvB-like 2 3.6.4.12 0.723
2ncd ADPProtein claret segregational / 0.721
3cph GDPRas-related protein SEC4 / 0.721
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.721
1oix GDPRas-related protein Rab-11A / 0.719
2fe4 GDPRas-related protein Rab-6B / 0.719
4ncl GDPEukaryotic translation initiation factor 5B / 0.719
1g16 GDPRas-related protein SEC4 / 0.718
1g6o ADPCag alpha / 0.718
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.718
2ce2 GDPGTPase HRas / 0.718
2zro ADPProtein RecA / 0.718
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.718
1f5n GNPGuanylate-binding protein 1 / 0.717
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.717
2zfi ADPKinesin-like protein KIF1A / 0.717
2g1q ADPKinesin-like protein KIF11 / 0.716
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.716
3ftq GNPSeptin-2 / 0.716
3ea5 GDPGTP-binding nuclear protein Ran / 0.715
4qbh AP5Adenylate kinase / 0.715
3zfd ANPChromosome-associated kinesin KIF4 / 0.714
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.713
5cyo GDPSeptin-9 / 0.713
4qbg AP5Adenylate kinase / 0.712
5ftc ADPTPR domain protein / 0.712
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.710
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.710
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
2zrj AGSProtein RecA / 0.710
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.708
1wbb ADPDNA mismatch repair protein MutS / 0.708
1zbd GTPRas-related protein Rab-3A / 0.708
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.706
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.705
3thy ADPDNA mismatch repair protein Msh2 / 0.702
4luc GDPGTPase KRas / 0.702
4o2l GTPGTP-binding protein Rheb / 0.702
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.701
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.701
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.701
3mjh GTPRas-related protein Rab-5A / 0.700
2cl6 CAGGTPase HRas / 0.699
3oiu GNPGTPase HRas / 0.699
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.697
1m7b GTPRho-related GTP-binding protein RhoE / 0.697
3k3b ADPKinesin-like protein KIF11 / 0.697
3tgp GNPGTPase HRas / 0.697
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.697
3vhx GTPADP-ribosylation factor 6 / 0.696
1zc3 GNPRas-related protein Ral-A / 0.695
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.693
2fna ADPUncharacterized protein / 0.693
4e07 ACPPlasmid partitioning protein ParF / 0.693
4yqf GDPSeptin-9 / 0.693
3c41 ANPAmino acid ABC transporter / 0.692
4dsu GDPGTPase KRas / 0.692
4ihq ADPConserved Archaeal protein / 0.692
4wa7 GDPGTPase KRas / 0.691
1l8q ADPChromosomal replication initiator protein DnaA / 0.690
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.690
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
2o8b ADPDNA mismatch repair protein Msh2 / 0.689
4ap0 ADPKinesin-like protein KIF11 / 0.689
1xmv ADPProtein RecA / 0.688
4jl5 ADPAdenylate kinase / 0.688
4y0v GDPADP-ribosylation factor 1, putative / 0.688
4ylg GDPADP-ribosylation factor 1, putative / 0.688
1rrg GDPADP-ribosylation factor 1 / 0.687
4iok ADPFormate--tetrahydrofolate ligase / 0.687
4xvu ATPATPase GET3 / 0.686
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.685
4nh0 ATPESX secretion system protein EccC / 0.685
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.685
3oee ANPATP synthase subunit alpha, mitochondrial / 0.683
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.683
2rgg GNPGTPase HRas / 0.682
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.682
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.681
4pfp ADPUnconventional myosin-VI / 0.681
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.680
2r9v ATPATP synthase subunit alpha / 0.680
3bxz ADPProtein translocase subunit SecA / 0.679
1jx2 ADPMyosin-2 heavy chain / 0.678
4d81 ADPAAA ATPase, central domain protein / 0.678
4db1 ANPMyosin-7 / 0.678
4i1v ADPDephospho-CoA kinase / 0.678
4jjz ADPFormate--tetrahydrofolate ligase / 0.678
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.678
5bn3 ADPV-type ATP synthase alpha chain / 0.678
5bn3 ADPNEQ263 / 0.678
2xae ADPKinesin-like protein KIF11 / 0.677
3zia ATPATP synthase subunit alpha, mitochondrial / 0.677
1lfd GNPGTPase HRas / 0.676
2dr3 ADPUPF0273 protein PH0284 / 0.676
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.676
3pcr GTPADP-ribosylation factor 6 / 0.676
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.674
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.674
1sxj ADPReplication factor C subunit 5 / 0.674
4gp6 ADPMetallophosphoesterase / 0.673
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.672
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
2qen ADPWalker-Type ATPase / 0.672
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.672
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.671
3qbv GDPCell division control protein 42 homolog / 0.671
1g41 ADPATP-dependent protease ATPase subunit HslU / 0.669
1w7i ADPUnconventional myosin-Va / 0.669
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.669
3b1x GNPFerrous iron transport protein B / 0.667
1ky2 GNPGTP-binding protein YPT7 / 0.666
2q3f GNPRas-related GTP-binding protein D / 0.666
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.666
4idn GNPAtlastin-1 3.6.5 0.666
1a4r GNHCell division control protein 42 homolog / 0.665
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.665
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.665
4xvr GNPGTPase HRas / 0.665
5fm6 ADPRuvB-like helicase / 0.665
1xp8 AGSProtein RecA / 0.664
3l1c ADPProtein claret segregational / 0.662
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.662
3oiw GNPGTPase HRas / 0.662
3qbt GNPRas-related protein Rab-8A / 0.662
4lj7 MNTChaperone protein ClpB / 0.662
1yra GDPGPN-loop GTPase PAB0955 / 0.661
3oes GNPGTPase RhebL1 / 0.661
4ohx ADPProtein clpf-1 / 0.661
1e4v AP5Adenylate kinase / 0.660
2iut AGSDNA translocase FtsK / 0.660
2j5x GSPADP-ribosylation factor 6 / 0.660
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
2xsz ATPRuvB-like 2 3.6.4.12 0.660
5d3q GDPDynamin-1 3.6.5.5 0.660
1yu9 GNPRas-related protein Rab-4A / 0.659
2q2y ADPKinesin-like protein KIF11 / 0.659
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.659
4xvq GNPGTPase HRas / 0.659
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.657
3tjz GNPADP-ribosylation factor 1 / 0.657
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.657
3law GNPRas-related protein Rab-7a / 0.656
3x1w GDPRas-related protein Rap-1b / 0.656
4x8l AP5Adenylate kinase / 0.656
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.655
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
2gm1 ADPKinesin-like protein KIF11 / 0.655
3kuc GDPRas-related protein Rap-1A / 0.655
3tnf GNPRas-related protein Rab-8A / 0.655
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.655
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.654
1ibr GNPGTP-binding nuclear protein Ran / 0.654
2vp4 DCPDeoxynucleoside kinase / 0.653
1w5s ADPORC1-type DNA replication protein 2 / 0.652
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.652
3q9l ATPSeptum site-determining protein MinD / 0.652
3r9i ADPSeptum site-determining protein MinD / 0.652
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.651
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.650
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.650
4dzz ADPPlasmid partitioning protein ParF / 0.650