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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
2eu8 AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2eu8 AP5Adenylate kinase / 1.879
2qaj AP5Adenylate kinase / 1.834
4mkg AP5Adenylate kinase / 1.725
2oo7 AP5Adenylate kinase / 1.650
2osb AP5Adenylate kinase / 1.575
3dkv AP5Adenylate kinase / 1.553
3dl0 AP5Adenylate kinase / 1.538
4nu0 AP5Adenylate kinase / 1.456
4w5j AP5Adenylate kinase / 1.365
4mkf AP5Adenylate kinase / 1.325
1p3j AP5Adenylate kinase / 1.293
2aky AP5Adenylate kinase / 1.142
1s3g AP5Adenylate kinase / 1.115
4tyq AP5Adenylate kinase / 1.113
4qbf AP5Adenylate kinase / 1.111
4qbh AP5Adenylate kinase / 1.099
4qbg AP5Adenylate kinase / 1.098
1zio AP5Adenylate kinase / 1.080
3aky AP5Adenylate kinase / 1.070
2rgx AP5Adenylate kinase / 1.064
4mkh AP5Adenylate kinase / 0.982
4qbi AP5Adenylate kinase / 0.968
4typ AP5Adenylate kinase / 0.949
4jld ADPAdenylate kinase / 0.829
4jky ADPAdenylate kinase / 0.814
4x8o AP5Adenylate kinase / 0.811
4jl5 ADPAdenylate kinase / 0.810
4jl8 ADPAdenylate kinase / 0.797
4jlb ADPAdenylate kinase / 0.790
4x8l AP5Adenylate kinase / 0.772
1svm ATPLarge T antigen 3.6.4 0.755
4qnr ATPPsp operon transcriptional activator / 0.733
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.726
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.721
1ake AP5Adenylate kinase / 0.720
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.719
2ffq GSPRas-related protein Rab-6B / 0.718
5d3q GDPDynamin-1 3.6.5.5 0.710
4e07 ACPPlasmid partitioning protein ParF / 0.707
1e4y AP5Adenylate kinase / 0.706
2hld ANPATP synthase subunit alpha, mitochondrial / 0.700
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.700
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.698
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.695
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.694
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.694
2gcp GSPRho-related GTP-binding protein RhoC / 0.689
3orl AGSSerine/threonine protein kinase / 0.688
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.686
1ank ANPAdenylate kinase / 0.682
1svw GTPProbable GTP-binding protein EngB / 0.680
4dxa GSPRas-related protein Rap-1b / 0.680
2a84 ATPPantothenate synthetase 6.3.2.1 0.678
3eg5 GNPCell division control protein 42 homolog / 0.678
2iut AGSDNA translocase FtsK / 0.677
1sxj AGSReplication factor C subunit 1 / 0.673
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.669
1e4v AP5Adenylate kinase / 0.668
2dpx GDPGTP-binding protein RAD / 0.668
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.668
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.667
4jlo ADPAdenylate kinase / 0.667
5jqg GTPTubulin alpha-1B chain / 0.667
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.665
1k5d GNPGTP-binding nuclear protein Ran / 0.664
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.664
1sq5 ADPPantothenate kinase 2.7.1.33 0.664
4y0v GDPADP-ribosylation factor 1, putative / 0.664
4cok TPPPyruvate decarboxylase / 0.663
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.660
1oe0 TTPDeoxynucleoside kinase / 0.659
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.659
5dac AGSUncharacterized protein / 0.659
1id0 ANPSensor protein PhoQ 2.7.13.3 0.658
3d7k D7KBenzaldehyde lyase / 0.658
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.658
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.658
1xs4 DCPdCTP deaminase / 0.657
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.657
1yrs ADPKinesin-like protein KIF11 / 0.655
2ggq TTPDual sugar-1-phosphate nucleotidylyltransferase / 0.655
4iij GTPTubulin alpha-1B chain / 0.655
4ol0 GTPGTP-binding nuclear protein Ran / 0.655
2cls GTPRho-related GTP-binding protein Rho6 / 0.654
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.653
2y6p CTP3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 0.653
4jla ADPAdenylate kinase / 0.653
3bc1 GNPRas-related protein Rab-27A / 0.652
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.651
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.651
3n0c FADFlavin-dependent thymidylate synthase 2.1.1.148 0.651
3ryh GTPTubulin alpha chain / 0.651
3w3z GTPGTP-binding nuclear protein Ran / 0.651
4asu ADPATP synthase subunit alpha, mitochondrial / 0.651
1w7i ADPUnconventional myosin-Va / 0.650
3law GNPRas-related protein Rab-7a / 0.650
4epw GDPGTPase KRas / 0.650
4kvg GTPRas-related protein Rap-1A / 0.650
4ylg GDPADP-ribosylation factor 1, putative / 0.650