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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
1p3j AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1p3j AP5Adenylate kinase / 1.785
3dl0 AP5Adenylate kinase / 1.397
2oo7 AP5Adenylate kinase / 1.332
4mkf AP5Adenylate kinase / 1.314
2eu8 AP5Adenylate kinase / 1.293
2qaj AP5Adenylate kinase / 1.222
1zio AP5Adenylate kinase / 1.198
4w5j AP5Adenylate kinase / 1.196
4mkg AP5Adenylate kinase / 1.141
1s3g AP5Adenylate kinase / 1.123
3dkv AP5Adenylate kinase / 1.123
2rgx AP5Adenylate kinase / 1.107
4qbh AP5Adenylate kinase / 1.079
2aky AP5Adenylate kinase / 1.069
3aky AP5Adenylate kinase / 1.065
4tyq AP5Adenylate kinase / 1.030
4mkh AP5Adenylate kinase / 0.978
2osb AP5Adenylate kinase / 0.962
4x8l AP5Adenylate kinase / 0.926
4x8o AP5Adenylate kinase / 0.901
4qbi AP5Adenylate kinase / 0.871
4jlo ADPAdenylate kinase / 0.870
4jl6 ADPAdenylate kinase / 0.859
4nu0 AP5Adenylate kinase / 0.856
3hpq AP5Adenylate kinase / 0.843
4jky ADPAdenylate kinase / 0.839
4qbf AP5Adenylate kinase / 0.831
4qbg AP5Adenylate kinase / 0.826
4jl5 ADPAdenylate kinase / 0.824
2bbw GP5Adenylate kinase 4, mitochondrial / 0.807
4typ AP5Adenylate kinase / 0.803
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.802
4qnr ATPPsp operon transcriptional activator / 0.795
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.790
1ake AP5Adenylate kinase / 0.776
1svm ATPLarge T antigen 3.6.4 0.775
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.774
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.768
4xsg GSPTransforming protein RhoA / 0.766
3kud GDPGTPase HRas / 0.765
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.765
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.763
2eck ADPAdenylate kinase / 0.761
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.761
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.760
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.759
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.756
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.753
2c9o ADPRuvB-like 1 3.6.4.12 0.750
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.749
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.749
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.749
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.747
4dzz ADPPlasmid partitioning protein ParF / 0.744
4g0n GNPGTPase HRas / 0.743
4jsy GTPMetallophosphoesterase / 0.741
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.739
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.738
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.737
4hse ADPChaperone protein ClpB / 0.737
2xsz ATPRuvB-like 2 3.6.4.12 0.734
3t1t GDPProbable gliding protein mglA / 0.733
4q02 GDPGTPase KRas / 0.733
4idn GNPAtlastin-1 3.6.5 0.732
4nh0 ATPESX secretion system protein EccC / 0.730
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.729
4jlb ADPAdenylate kinase / 0.729
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.728
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.728
3hpr AP5Adenylate kinase / 0.725
2vf7 ADPUvrABC system protein A / 0.718
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.715
1w5t ADPORC1-type DNA replication protein 2 / 0.714
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.713
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.712
1z6t ADPApoptotic protease-activating factor 1 / 0.711
3ieu GDPGTPase Era / 0.711
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.710
4qm6 GTPMetallophosphoesterase / 0.709
2ql6 ADPNicotinamide riboside kinase 1 / 0.707
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.706
4c30 ANPDNA helicase / 0.706
3d8b ADPFidgetin-like protein 1 3.6.4 0.705
3tjz GNPADP-ribosylation factor 1 / 0.705
4jlp ADPAdenylate kinase / 0.703
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.700
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.697
3tlx ADPAdenylate kinase 2 / 0.697
4jl8 ADPAdenylate kinase / 0.697
1mab ATPATP synthase subunit alpha, mitochondrial / 0.694
5d3q GDPDynamin-1 3.6.5.5 0.693
5dac AGSUncharacterized protein / 0.693
1z0a GDPRas-related protein Rab-2A / 0.692
4ike ADPAdenylate kinase / 0.691
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.690
3kz1 GSPTransforming protein RhoA / 0.690
4dvg GSPRho family GTPase / 0.690
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.689
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.689
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.685
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.685
3wyf GTPGTP-binding nuclear protein / 0.685
1svw GTPProbable GTP-binding protein EngB / 0.684
3m0e ATPTranscriptional regulator (NtrC family) / 0.684
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.682
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.682
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.680
1sxj AGSReplication factor C subunit 1 / 0.679
4ihq ADPConserved Archaeal protein / 0.679
4o2r GDPGTP-binding protein Rheb / 0.679
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.678
1ii6 ADPKinesin-like protein KIF11 / 0.677
2cls GTPRho-related GTP-binding protein Rho6 / 0.676
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.676
1oe0 TTPDeoxynucleoside kinase / 0.675
4qos ADPPsp operon transcriptional activator / 0.674
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.671
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.669
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.668
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.668
3r9x GNPGTPase Era / 0.668
4ol0 GTPGTP-binding nuclear protein Ran / 0.668
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.667
1wbb ADPDNA mismatch repair protein MutS / 0.667
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.667
1p52 ADPArginine kinase 2.7.3.3 0.666
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.666
4khy TTPDNA-directed DNA polymerase / 0.666
4yqf GDPSeptin-9 / 0.665
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.664
3c41 ANPAmino acid ABC transporter / 0.664
3orl AGSSerine/threonine protein kinase / 0.664
4o4l GTPTubulin alpha-1B chain / 0.664
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.663
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.663
1n6m ADPProtein claret segregational / 0.662
1zm7 TTPDeoxynucleoside kinase / 0.662
1wdt GTPElongation factor G (EF-G-2) / 0.661
4wbn GTPTubulin alpha-1B chain / 0.659
4zol GTPTubulin alpha-1B chain / 0.659
2a84 ATPPantothenate synthetase 6.3.2.1 0.658
1sq5 ADPPantothenate kinase 2.7.1.33 0.657
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.657
3pcr GTPADP-ribosylation factor 6 / 0.657
5itz GTPTubulin alpha-1B chain / 0.657
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.656
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.656
1k5d GNPGTP-binding nuclear protein Ran / 0.655
1t91 GTPRas-related protein Rab-7a / 0.655
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.655
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.654
4qfx DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.654
4ww4 ADPRuvB-like helicase / 0.653
4yj2 GTPTubulin alpha-1B chain / 0.653
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.652
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.652
2y6p CTP3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 0.652
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.652
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.652
5fl3 ADPPili retraction protein PilT / 0.652
2a5y ATPCell death protein 4 / 0.651
2gil GTPRas-related protein Rab-6A / 0.651
3uk6 ADPRuvB-like 2 3.6.4.12 0.650