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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
4mkf AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4mkf AP5Adenylate kinase / 1.863
4mkg AP5Adenylate kinase / 1.662
2qaj AP5Adenylate kinase / 1.430
4w5j AP5Adenylate kinase / 1.392
2osb AP5Adenylate kinase / 1.372
2oo7 AP5Adenylate kinase / 1.363
4tyq AP5Adenylate kinase / 1.359
4nu0 AP5Adenylate kinase / 1.331
3dl0 AP5Adenylate kinase / 1.329
2eu8 AP5Adenylate kinase / 1.325
1p3j AP5Adenylate kinase / 1.314
2aky AP5Adenylate kinase / 1.303
3dkv AP5Adenylate kinase / 1.295
3aky AP5Adenylate kinase / 1.286
1zio AP5Adenylate kinase / 1.157
4qbh AP5Adenylate kinase / 1.095
4qbg AP5Adenylate kinase / 1.069
2rgx AP5Adenylate kinase / 1.057
4qbf AP5Adenylate kinase / 1.010
4qbi AP5Adenylate kinase / 0.980
4mkh AP5Adenylate kinase / 0.953
1e4v AP5Adenylate kinase / 0.945
4qm6 GTPMetallophosphoesterase / 0.934
4jl6 ADPAdenylate kinase / 0.911
4jlo ADPAdenylate kinase / 0.908
4jky ADPAdenylate kinase / 0.893
4x8l AP5Adenylate kinase / 0.885
4jl5 ADPAdenylate kinase / 0.878
4jld ADPAdenylate kinase / 0.875
4typ AP5Adenylate kinase / 0.864
3hpq AP5Adenylate kinase / 0.838
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.823
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.821
1ake AP5Adenylate kinase / 0.819
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.803
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.801
1a2b GSPTransforming protein RhoA / 0.796
1s3g AP5Adenylate kinase / 0.796
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.785
1cxz GSPTransforming protein RhoA / 0.781
4qos ADPPsp operon transcriptional activator / 0.779
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.775
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.771
1t91 GTPRas-related protein Rab-7a / 0.769
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.769
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.769
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.764
4k81 GTPGTPase HRas / 0.763
2eck ADPAdenylate kinase / 0.762
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.761
4epx GDPGTPase KRas / 0.761
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.760
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.757
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.756
1wbb ADPDNA mismatch repair protein MutS / 0.755
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.755
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.754
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.752
1gwn GTPRho-related GTP-binding protein RhoE / 0.746
4kvg GTPRas-related protein Rap-1A / 0.746
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.745
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.743
2hld ANPATP synthase subunit alpha, mitochondrial / 0.743
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.743
1fmw ATPMyosin-2 heavy chain / 0.742
2ffq GSPRas-related protein Rab-6B / 0.741
2vp0 TTPDeoxynucleoside kinase / 0.738
3tlx ADPAdenylate kinase 2 / 0.736
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.735
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.734
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.734
2c9o ADPRuvB-like 1 3.6.4.12 0.734
2zet GTPRas-related protein Rab-27B / 0.734
4jlb ADPAdenylate kinase / 0.734
4obe GDPGTPase KRas / 0.733
1svm ATPLarge T antigen 3.6.4 0.732
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.732
1dvr ATFAdenylate kinase / 0.731
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.731
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.731
4oi2 ADPProtein clpf-1 / 0.730
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.728
2gcp GSPRho-related GTP-binding protein RhoC / 0.728
4d0l GSPRas-related protein Rab-11A / 0.727
2vf7 ADPUvrABC system protein A / 0.726
4i1v ADPDephospho-CoA kinase / 0.726
1g16 GDPRas-related protein SEC4 / 0.725
3kz1 GSPTransforming protein RhoA / 0.725
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.724
1oe0 TTPDeoxynucleoside kinase / 0.720
5da9 AGSUncharacterized protein / 0.720
1rrg GDPADP-ribosylation factor 1 / 0.718
4c30 ANPDNA helicase / 0.718
4hse ADPChaperone protein ClpB / 0.718
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.717
4dso GSPGTPase KRas / 0.717
5c46 GSPRas-related protein Rab-11A / 0.717
4jl8 ADPAdenylate kinase / 0.715
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.714
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.714
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.714
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.714
1l8q ADPChromosomal replication initiator protein DnaA / 0.713
2r9v ATPATP synthase subunit alpha / 0.713
3l1c ADPProtein claret segregational / 0.711
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.711
5dac AGSUncharacterized protein / 0.711
2jcs TTPDeoxynucleoside kinase / 0.710
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.708
3d8b ADPFidgetin-like protein 1 3.6.4 0.708
3q5d GDPAtlastin-1 3.6.5 0.707
1svw GTPProbable GTP-binding protein EngB / 0.706
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.706
2x7e ADPKinesin-like protein KIF11 / 0.706
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.705
3k3b ADPKinesin-like protein KIF11 / 0.705
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.704
4dvg GSPRho family GTPase / 0.704
2ql6 ADPNicotinamide riboside kinase 1 / 0.703
4asu ADPATP synthase subunit alpha, mitochondrial / 0.703
4ike ADPAdenylate kinase / 0.703
4b7b ADPKinesin-like protein KIF11 / 0.701
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.701
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.700
4zca ADPKinesin-like protein KIF11 / 0.700
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.699
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.699
1sq5 ADPPantothenate kinase 2.7.1.33 0.697
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.696
4dzz ADPPlasmid partitioning protein ParF / 0.696
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.695
3orl AGSSerine/threonine protein kinase / 0.695
3m0e ATPTranscriptional regulator (NtrC family) / 0.694
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.694
1xts GTPGTP-binding protein Rheb / 0.693
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.692
2pg2 ADPKinesin-like protein KIF11 / 0.692
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.692
1esn ANPPantothenate kinase 2.7.1.33 0.691
1w5s ADPORC1-type DNA replication protein 2 / 0.691
2fl2 ADPKinesin-like protein KIF11 / 0.691
2q2z ADPKinesin-like protein KIF11 / 0.691
4ihq ADPConserved Archaeal protein / 0.691
4x8o AP5Adenylate kinase / 0.691
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.689
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.688
2xsz ATPRuvB-like 2 3.6.4.12 0.687
4idp GNPAtlastin-1 3.6.5 0.687
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.686
4cf7 ADPAdenylate kinase / 0.686
3zia ATPATP synthase subunit alpha, mitochondrial / 0.685
2a84 ATPPantothenate synthetase 6.3.2.1 0.684
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.684
2x3j ATPAcsD / 0.684
5itz GTPTubulin alpha-1B chain / 0.684
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.683
3ref GDPRho family GTPase / 0.683
4o25 GTPGTP-binding protein Rheb / 0.683
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.682
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.681
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.680
4ylg GDPADP-ribosylation factor 1, putative / 0.680
4brd ANPEctonucleoside triphosphate diphosphohydrolase I / 0.679
1bxr ANPCarbamoyl-phosphate synthase large chain / 0.678
4yj2 GTPTubulin alpha-1B chain / 0.677
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.675
4qfy DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.675
1kqm ANPMyosin heavy chain, striated muscle / 0.674
2bbw GP5Adenylate kinase 4, mitochondrial / 0.674
2dft ADPShikimate kinase 2.7.1.71 0.674
2g1q ADPKinesin-like protein KIF11 / 0.674
3l9h ADPKinesin-like protein KIF11 / 0.674
4ohw ATPProtein clpf-1 / 0.674
4o2r GDPGTP-binding protein Rheb / 0.673
4tnq TTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.673
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.672
3d7k D7KBenzaldehyde lyase / 0.672
4jlp ADPAdenylate kinase / 0.672
1z6t ADPApoptotic protease-activating factor 1 / 0.671
4ol0 GTPGTP-binding nuclear protein Ran / 0.671
3pcr GTPADP-ribosylation factor 6 / 0.670
4l16 ADPFidgetin-like protein 1 3.6.4 0.670
1u9i ATPCircadian clock protein kinase KaiC 2.7.11.1 0.669
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.668
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.668
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
1b7t ADPMyosin heavy chain, striated muscle / 0.667
3wyf GTPGTP-binding nuclear protein / 0.667
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.667
2c9c ATPPsp operon transcriptional activator / 0.666
2q3f GNPRas-related GTP-binding protein D / 0.666
4tq9 GDPGTPase KRas / 0.666
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.666
2y6p CTP3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 0.665
3myk ANPMyosin-2 heavy chain / 0.665
4brg GNPEctonucleoside triphosphate diphosphohydrolase I / 0.665
4ww4 ADPRuvB-like helicase / 0.664
4y0v GDPADP-ribosylation factor 1, putative / 0.664
1ii6 ADPKinesin-like protein KIF11 / 0.663
3c41 ANPAmino acid ABC transporter / 0.662
1a4r GNHCell division control protein 42 homolog / 0.661
5fm6 ADPRuvB-like helicase / 0.661
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.660
1sxj AGSReplication factor C subunit 1 / 0.660
3k0f ATPCircadian clock protein kinase KaiC 2.7.11.1 0.660
4fvq ATPTyrosine-protein kinase JAK2 / 0.660
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.660
4tv9 GTPTubulin alpha-1B chain / 0.660
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.659
2dr3 ADPUPF0273 protein PH0284 / 0.659
3krf DSTGeranyl diphosphate synthase large subunit / 0.659
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.659
3ruq ADPChaperonin / 0.658
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.658
1rj9 GCPSignal recognition particle receptor FtsY / 0.657
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.656
2l0x GDPGTP-binding protein Rheb / 0.656
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.656
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.656
4n57 ADPAPH(2'')-Id / 0.656
4zol GTPTubulin alpha-1B chain / 0.656
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.655
4ihj GTPTubulin alpha-1B chain / 0.655
1tf7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.654
4h5e YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.654
4iei ADPGene 2 protein / 0.654
4xoi GTPTransforming protein RhoA / 0.654
2fg5 GNPRas-related protein Rab-31 / 0.653
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
2xto GDPGTPase IMAP family member 2 / 0.653
3s8a DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.653
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.653
4wbn GTPTubulin alpha-1B chain / 0.653
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.652
2z4w 749Geranylgeranyl pyrophosphate synthase / 0.652
3hpr AP5Adenylate kinase / 0.652
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.652
1ank ANPAdenylate kinase / 0.651
2cls GTPRho-related GTP-binding protein Rho6 / 0.651
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.651
3oee ANPATP synthase subunit alpha, mitochondrial / 0.651
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.651
1pow TPPPyruvate oxidase 1.2.3.3 0.650
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.650
3mhy ATPNitrogen regulatory protein P-II 1 / 0.650
3uk6 ADPRuvB-like 2 3.6.4.12 0.650