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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
2aky AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2aky AP5Adenylate kinase / 1.881
3aky AP5Adenylate kinase / 1.685
4mkg AP5Adenylate kinase / 1.444
3dkv AP5Adenylate kinase / 1.328
2oo7 AP5Adenylate kinase / 1.304
4mkf AP5Adenylate kinase / 1.303
4nu0 AP5Adenylate kinase / 1.301
3dl0 AP5Adenylate kinase / 1.292
2qaj AP5Adenylate kinase / 1.238
2osb AP5Adenylate kinase / 1.169
2eu8 AP5Adenylate kinase / 1.142
4w5j AP5Adenylate kinase / 1.131
4tyq AP5Adenylate kinase / 1.097
1p3j AP5Adenylate kinase / 1.069
1zio AP5Adenylate kinase / 1.057
2rgx AP5Adenylate kinase / 1.017
1s3g AP5Adenylate kinase / 0.926
4qbf AP5Adenylate kinase / 0.916
4mkh AP5Adenylate kinase / 0.915
3hpq AP5Adenylate kinase / 0.891
4x8l AP5Adenylate kinase / 0.831
4jl8 ADPAdenylate kinase / 0.822
4ike ADPAdenylate kinase / 0.792
4typ AP5Adenylate kinase / 0.792
1svm ATPLarge T antigen 3.6.4 0.790
4x8o AP5Adenylate kinase / 0.790
4jl5 ADPAdenylate kinase / 0.782
4jky ADPAdenylate kinase / 0.781
4jl6 ADPAdenylate kinase / 0.772
4jlo ADPAdenylate kinase / 0.771
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.765
4jld ADPAdenylate kinase / 0.762
4jlp ADPAdenylate kinase / 0.756
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.755
4jsy GTPMetallophosphoesterase / 0.755
2ffq GSPRas-related protein Rab-6B / 0.747
3hpr AP5Adenylate kinase / 0.745
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.742
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.740
4jlb ADPAdenylate kinase / 0.740
4qbh AP5Adenylate kinase / 0.736
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.730
4qbg AP5Adenylate kinase / 0.729
1fmw ATPMyosin-2 heavy chain / 0.728
4jla ADPAdenylate kinase / 0.727
1ake AP5Adenylate kinase / 0.722
1mmg AGSMyosin-2 heavy chain / 0.720
2gcp GSPRho-related GTP-binding protein RhoC / 0.709
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.709
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.707
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.707
2eck ADPAdenylate kinase / 0.706
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.703
1e4v AP5Adenylate kinase / 0.700
4k81 GTPGTPase HRas / 0.695
3q5d GDPAtlastin-1 3.6.5 0.693
1e4y AP5Adenylate kinase / 0.692
1dvr ATFAdenylate kinase / 0.690
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.690
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
4xsg GSPTransforming protein RhoA / 0.686
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.684
4yj2 GTPTubulin alpha-1B chain / 0.684
4qbi AP5Adenylate kinase / 0.683
5c46 GSPRas-related protein Rab-11A / 0.683
5i4n ATPTyrosine-protein kinase JAK2 / 0.683
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.682
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.678
2a5y ATPCell death protein 4 / 0.678
4fvq ATPTyrosine-protein kinase JAK2 / 0.678
5ios FADFlavin-dependent thymidylate synthase 2.1.1.148 0.678
4qm6 GTPMetallophosphoesterase / 0.677
1a2b GSPTransforming protein RhoA / 0.676
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.675
5jqg GTPTubulin alpha-1B chain / 0.675
1wdt GTPElongation factor G (EF-G-2) / 0.672
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.672
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.672
1b7t ADPMyosin heavy chain, striated muscle / 0.671
4dvg GSPRho family GTPase / 0.671
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.671
1ny5 ADPTranscriptional regulator (NtrC family) / 0.670
1wa5 GTPGTP-binding nuclear protein Ran / 0.670
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.670
3orl AGSSerine/threonine protein kinase / 0.670
3pcr GTPADP-ribosylation factor 6 / 0.670
4b7b ADPKinesin-like protein KIF11 / 0.670
1svw GTPProbable GTP-binding protein EngB / 0.668
4ol0 GTPGTP-binding nuclear protein Ran / 0.668
3wyf GTPGTP-binding nuclear protein / 0.667
4xoi GTPTransforming protein RhoA / 0.667
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.666
3tqc ADPPantothenate kinase / 0.665
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.664
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
4cf7 ADPAdenylate kinase / 0.664
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.663
3n0c FADFlavin-dependent thymidylate synthase 2.1.1.148 0.663
4zol GTPTubulin alpha-1B chain / 0.663
3rv4 ADPBiotin carboxylase 6.3.4.14 0.662
4yqf GDPSeptin-9 / 0.662
2y6p CTP3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 0.661
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.661
1oe0 TTPDeoxynucleoside kinase / 0.659
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.659
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.658
3mvw BHZNickel-binding periplasmic protein / 0.658
3ruq ADPChaperonin / 0.657
4kvg GTPRas-related protein Rap-1A / 0.657
2hld ANPATP synthase subunit alpha, mitochondrial / 0.656
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.656
4qxa GTPRas-related protein Rab-9A / 0.656
1xts GTPGTP-binding protein Rheb / 0.655
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.655
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.654
4qfy DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.654
2q9c GNPSignal recognition particle receptor FtsY / 0.653
1yqd NAPSinapyl alcohol dehydrogenase / 0.652
4fh5 UTPTerminal uridylyltransferase cid1 / 0.651
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.651
4qnr ATPPsp operon transcriptional activator / 0.651
1w5a GTPCell division protein FtsZ 1 / 0.650
1zbd GTPRas-related protein Rab-3A / 0.650
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
4mit GTPRho-related protein racC / 0.650
4zca ADPKinesin-like protein KIF11 / 0.650