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
1zio AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1zio AP5Adenylate kinase / 1.641
3dl0 AP5Adenylate kinase / 1.343
4tyq AP5Adenylate kinase / 1.272
1p3j AP5Adenylate kinase / 1.198
4mkf AP5Adenylate kinase / 1.157
2oo7 AP5Adenylate kinase / 1.139
2eu8 AP5Adenylate kinase / 1.080
2qaj AP5Adenylate kinase / 1.065
4mkg AP5Adenylate kinase / 1.062
2aky AP5Adenylate kinase / 1.057
4mkh AP5Adenylate kinase / 1.024
2rgx AP5Adenylate kinase / 1.021
3aky AP5Adenylate kinase / 0.980
3dkv AP5Adenylate kinase / 0.976
2osb AP5Adenylate kinase / 0.961
4qbg AP5Adenylate kinase / 0.938
1s3g AP5Adenylate kinase / 0.917
4w5j AP5Adenylate kinase / 0.915
4qbf AP5Adenylate kinase / 0.909
4qbh AP5Adenylate kinase / 0.892
4nu0 AP5Adenylate kinase / 0.876
4qbi AP5Adenylate kinase / 0.838
4ike ADPAdenylate kinase / 0.817
1e4v AP5Adenylate kinase / 0.808
4jl5 ADPAdenylate kinase / 0.800
4jld ADPAdenylate kinase / 0.796
3hpr AP5Adenylate kinase / 0.795
2eck ADPAdenylate kinase / 0.792
2r9v ATPATP synthase subunit alpha / 0.786
4jl6 ADPAdenylate kinase / 0.784
3tlx ADPAdenylate kinase 2 / 0.782
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.780
4qos ADPPsp operon transcriptional activator / 0.778
4jl8 ADPAdenylate kinase / 0.775
4qnr ATPPsp operon transcriptional activator / 0.771
2gcp GSPRho-related GTP-binding protein RhoC / 0.770
2hld ANPATP synthase subunit alpha, mitochondrial / 0.765
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.765
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.762
4x8o AP5Adenylate kinase / 0.757
1am4 GNPCell division control protein 42 homolog / 0.756
4jlb ADPAdenylate kinase / 0.754
3kz1 GSPTransforming protein RhoA / 0.751
3r9i ADPSeptum site-determining protein MinD / 0.749
4dvg GSPRho family GTPase / 0.747
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.746
5fl3 ADPPili retraction protein PilT / 0.745
4jlo ADPAdenylate kinase / 0.743
4typ AP5Adenylate kinase / 0.743
4idn GNPAtlastin-1 3.6.5 0.742
4mit GTPRho-related protein racC / 0.742
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.738
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.736
1fnn ADPORC1-type DNA replication protein / 0.734
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.734
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.731
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.727
3d8b ADPFidgetin-like protein 1 3.6.4 0.727
2c96 ATPPsp operon transcriptional activator / 0.722
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.718
5ftf ADPTPR domain protein / 0.717
5cyo GDPSeptin-9 / 0.716
4jlp ADPAdenylate kinase / 0.715
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.712
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.712
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.711
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.711
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.710
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
4d81 ADPAAA ATPase, central domain protein / 0.707
1ii6 ADPKinesin-like protein KIF11 / 0.706
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.705
4ohv ANPProtein clpf-1 / 0.705
4x8l AP5Adenylate kinase / 0.705
3t1t GDPProbable gliding protein mglA / 0.703
3l9h ADPKinesin-like protein KIF11 / 0.701
4jla ADPAdenylate kinase / 0.701
4hse ADPChaperone protein ClpB / 0.700
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.699
5d3q GDPDynamin-1 3.6.5.5 0.696
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.695
3k1j ADPATP-dependent protease Lon / 0.693
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.692
5c46 GSPRas-related protein Rab-11A / 0.692
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.691
4jky ADPAdenylate kinase / 0.691
1ny5 ADPTranscriptional regulator (NtrC family) / 0.690
1v8k ANPKinesin-like protein KIF2C / 0.690
4qm6 GTPMetallophosphoesterase / 0.689
2a5y ATPCell death protein 4 / 0.688
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.688
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.688
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.686
4iei ADPGene 2 protein / 0.685
3fkq ATPNtrC-like two-domain protein / 0.684
4b7b ADPKinesin-like protein KIF11 / 0.684
2x3j ATPAcsD / 0.683
4xoi GTPTransforming protein RhoA / 0.683
1mab ATPATP synthase subunit alpha, mitochondrial / 0.682
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.681
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.677
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.677
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.677
3l1c ADPProtein claret segregational / 0.677
4oi2 ADPProtein clpf-1 / 0.677
1p9w ANPType II secretion system protein E / 0.676
2npi ATPmRNA cleavage and polyadenylation factor CLP1 / 0.675
2vf7 ADPUvrABC system protein A / 0.674
2fl2 ADPKinesin-like protein KIF11 / 0.673
1z6t ADPApoptotic protease-activating factor 1 / 0.672
3zia ATPATP synthase subunit alpha, mitochondrial / 0.670
4ww4 ADPRuvB-like helicase / 0.668
3pcr GTPADP-ribosylation factor 6 / 0.666
3vtk ADPThymidine kinase / 0.666
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.665
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.665
4iok ADPFormate--tetrahydrofolate ligase / 0.665
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.664
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.664
2ql6 ADPNicotinamide riboside kinase 1 / 0.664
3c41 ANPAmino acid ABC transporter / 0.664
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.663
2xtn GTPGTPase IMAP family member 2 / 0.663
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.662
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.660
1mmg AGSMyosin-2 heavy chain / 0.659
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.659
3eg5 GNPCell division control protein 42 homolog / 0.659
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.659
3thy ADPDNA mismatch repair protein Msh2 / 0.659
4ol0 GTPGTP-binding nuclear protein Ran / 0.659
2zrj AGSProtein RecA / 0.658
1t91 GTPRas-related protein Rab-7a / 0.657
1wa5 GTPGTP-binding nuclear protein Ran / 0.657
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.656
1ake AP5Adenylate kinase / 0.655
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.654
1e4y AP5Adenylate kinase / 0.654
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.654
4rz3 ADPSite-determining protein / 0.654
1ih8 APCNH(3)-dependent NAD(+) synthetase 6.3.1.5 0.653
4kvg GTPRas-related protein Rap-1A / 0.653
2bbw GP5Adenylate kinase 4, mitochondrial / 0.652
3oee ANPATP synthase subunit alpha, mitochondrial / 0.652
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
5dac AGSUncharacterized protein / 0.652
1svw GTPProbable GTP-binding protein EngB / 0.651
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.651
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.651
1cxz GSPTransforming protein RhoA / 0.650
1zbd GTPRas-related protein Rab-3A / 0.650
2cls GTPRho-related GTP-binding protein Rho6 / 0.650
3orl AGSSerine/threonine protein kinase / 0.650