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
4tyq AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4tyq AP5Adenylate kinase / 1.807
4mkf AP5Adenylate kinase / 1.359
1zio AP5Adenylate kinase / 1.272
3dl0 AP5Adenylate kinase / 1.207
2eu8 AP5Adenylate kinase / 1.113
2aky AP5Adenylate kinase / 1.097
4mkg AP5Adenylate kinase / 1.062
2qaj AP5Adenylate kinase / 1.054
1p3j AP5Adenylate kinase / 1.030
4qbg AP5Adenylate kinase / 1.030
3aky AP5Adenylate kinase / 1.023
2osb AP5Adenylate kinase / 1.015
2oo7 AP5Adenylate kinase / 0.985
2rgx AP5Adenylate kinase / 0.934
3dkv AP5Adenylate kinase / 0.891
4mkh AP5Adenylate kinase / 0.878
4nu0 AP5Adenylate kinase / 0.866
1s3g AP5Adenylate kinase / 0.863
4w5j AP5Adenylate kinase / 0.857
4qbi AP5Adenylate kinase / 0.842
4qbh AP5Adenylate kinase / 0.838
4x8l AP5Adenylate kinase / 0.827
4ike ADPAdenylate kinase / 0.806
2ffq GSPRas-related protein Rab-6B / 0.801
3tlx ADPAdenylate kinase 2 / 0.800
4jl5 ADPAdenylate kinase / 0.798
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.791
1a2b GSPTransforming protein RhoA / 0.781
4qos ADPPsp operon transcriptional activator / 0.778
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.773
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.770
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.769
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.769
2gm1 ADPKinesin-like protein KIF11 / 0.766
4xsg GSPTransforming protein RhoA / 0.766
2gcp GSPRho-related GTP-binding protein RhoC / 0.765
4jld ADPAdenylate kinase / 0.763
4jlo ADPAdenylate kinase / 0.761
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.759
1wdt GTPElongation factor G (EF-G-2) / 0.757
1cxz GSPTransforming protein RhoA / 0.754
2r9v ATPATP synthase subunit alpha / 0.752
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.749
4pfp ADPUnconventional myosin-VI / 0.748
4jky ADPAdenylate kinase / 0.747
4pjk ADPMyosin-2 heavy chain / 0.747
4jl6 ADPAdenylate kinase / 0.746
4qnr ATPPsp operon transcriptional activator / 0.746
4qbf AP5Adenylate kinase / 0.745
1z6t ADPApoptotic protease-activating factor 1 / 0.744
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.742
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.739
2eck ADPAdenylate kinase / 0.737
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.736
1svm ATPLarge T antigen 3.6.4 0.735
2zfi ADPKinesin-like protein KIF1A / 0.734
3b1x GNPFerrous iron transport protein B / 0.734
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.733
4ww4 ADPRuvB-like helicase / 0.733
4x8o AP5Adenylate kinase / 0.732
4dzz ADPPlasmid partitioning protein ParF / 0.729
4typ AP5Adenylate kinase / 0.729
5c46 GSPRas-related protein Rab-11A / 0.729
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.728
4jsy GTPMetallophosphoesterase / 0.728
1yrs ADPKinesin-like protein KIF11 / 0.724
2vf7 ADPUvrABC system protein A / 0.724
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.723
1ank ANPAdenylate kinase / 0.722
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.722
4hse ADPChaperone protein ClpB / 0.722
4idn GNPAtlastin-1 3.6.5 0.722
5aun ADPIron-sulfur cluster carrier protein / 0.721
1e4v AP5Adenylate kinase / 0.720
4dxa GSPRas-related protein Rap-1b / 0.720
1am4 GNPCell division control protein 42 homolog / 0.719
1rrg GDPADP-ribosylation factor 1 / 0.719
2c9o ADPRuvB-like 1 3.6.4.12 0.719
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.719
4c2u ANPDNA helicase / 0.719
4jl8 ADPAdenylate kinase / 0.719
4yqf GDPSeptin-9 / 0.719
4a51 ADPKinesin-like protein KIF11 / 0.718
4c30 ANPDNA helicase / 0.718
4jlp ADPAdenylate kinase / 0.718
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.717
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.716
2cls GTPRho-related GTP-binding protein Rho6 / 0.715
2l0x GDPGTP-binding protein Rheb / 0.714
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.714
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.713
2ql6 ADPNicotinamide riboside kinase 1 / 0.713
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.712
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.711
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.709
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.709
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.708
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
3d8b ADPFidgetin-like protein 1 3.6.4 0.708
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.708
2xae ADPKinesin-like protein KIF11 / 0.706
4g0n GNPGTPase HRas / 0.706
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.704
4gp6 ADPMetallophosphoesterase / 0.704
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.701
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.700
3k3b ADPKinesin-like protein KIF11 / 0.699
3l9h ADPKinesin-like protein KIF11 / 0.698
5d3q GDPDynamin-1 3.6.5.5 0.697
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.692
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.692
5i4n ATPTyrosine-protein kinase JAK2 / 0.692
1sxj AGSReplication factor C subunit 1 / 0.691
2g1q ADPKinesin-like protein KIF11 / 0.689
2vp0 TTPDeoxynucleoside kinase / 0.689
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.688
1mab ATPATP synthase subunit alpha, mitochondrial / 0.688
2a5y ATPCell death protein 4 / 0.688
3orl AGSSerine/threonine protein kinase / 0.688
4k81 GTPGTPase HRas / 0.688
4zca ADPKinesin-like protein KIF11 / 0.688
4mit GTPRho-related protein racC / 0.687
2fl2 ADPKinesin-like protein KIF11 / 0.686
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.685
3ryh GTPTubulin alpha chain / 0.683
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.682
4jlb ADPAdenylate kinase / 0.682
2jcs TTPDeoxynucleoside kinase / 0.681
3law GNPRas-related protein Rab-7a / 0.680
3m0e ATPTranscriptional regulator (NtrC family) / 0.680
1e4y AP5Adenylate kinase / 0.679
2pg2 ADPKinesin-like protein KIF11 / 0.678
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.678
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.677
2x2r ADPKinesin-like protein KIF11 / 0.677
4ol0 GTPGTP-binding nuclear protein Ran / 0.677
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.676
4fvr ATPTyrosine-protein kinase JAK2 / 0.676
5fl3 ADPPili retraction protein PilT / 0.676
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.675
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.675
5bn4 ANPV-type ATP synthase alpha chain / 0.675
2uyi ADPKinesin-like protein KIF11 / 0.674
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.674
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.674
1ii6 ADPKinesin-like protein KIF11 / 0.672
3fkq ATPNtrC-like two-domain protein / 0.672
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.671
4rz3 ADPSite-determining protein / 0.671
5dac AGSUncharacterized protein / 0.671
3pcr GTPADP-ribosylation factor 6 / 0.670
3zia ATPATP synthase subunit alpha, mitochondrial / 0.670
1oe0 TTPDeoxynucleoside kinase / 0.669
2jlr ANPGenome polyprotein 3.4.21.91 0.669
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.669
1xje TTPVitamin B12-dependent ribonucleotide reductase / 0.668
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.668
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.665
4tv9 GTPTubulin alpha-1B chain / 0.665
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.665
2y6p CTP3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 0.664
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.664
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.664
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.664
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.663
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.663
3c41 ANPAmino acid ABC transporter / 0.662
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.662
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.662
4ohv ANPProtein clpf-1 / 0.661
4jla ADPAdenylate kinase / 0.660
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.659
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.659
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.658
2c5l GTPGTPase HRas / 0.657
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.657
3wyf GTPGTP-binding nuclear protein / 0.657
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.655
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
1n75 ATPGlutamate--tRNA ligase 6.1.1.17 0.654
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.654
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.654
4ffb GTPTubulin alpha-1 chain / 0.650
4gvz ADPArginine kinase 2.7.3.3 0.650