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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
4nu0 AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4nu0 AP5Adenylate kinase / 1.806
4mkg AP5Adenylate kinase / 1.482
2eu8 AP5Adenylate kinase / 1.456
2oo7 AP5Adenylate kinase / 1.454
3dkv AP5Adenylate kinase / 1.443
3dl0 AP5Adenylate kinase / 1.410
2qaj AP5Adenylate kinase / 1.370
4mkf AP5Adenylate kinase / 1.331
4w5j AP5Adenylate kinase / 1.325
2aky AP5Adenylate kinase / 1.301
3aky AP5Adenylate kinase / 1.234
2osb AP5Adenylate kinase / 1.221
4qbh AP5Adenylate kinase / 1.068
4typ AP5Adenylate kinase / 1.059
4qbg AP5Adenylate kinase / 0.950
1s3g AP5Adenylate kinase / 0.931
4qbf AP5Adenylate kinase / 0.892
1zio AP5Adenylate kinase / 0.876
4tyq AP5Adenylate kinase / 0.866
1p3j AP5Adenylate kinase / 0.856
4jlb ADPAdenylate kinase / 0.844
4qm6 GTPMetallophosphoesterase / 0.835
4jlp ADPAdenylate kinase / 0.816
1svm ATPLarge T antigen 3.6.4 0.793
4qbi AP5Adenylate kinase / 0.791
1e4v AP5Adenylate kinase / 0.773
4jl8 ADPAdenylate kinase / 0.764
3hpq AP5Adenylate kinase / 0.759
3wyf GTPGTP-binding nuclear protein / 0.755
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.748
2rgx AP5Adenylate kinase / 0.742
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.733
4mkh AP5Adenylate kinase / 0.732
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.723
2xtn GTPGTPase IMAP family member 2 / 0.718
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.716
4x8l AP5Adenylate kinase / 0.715
3mjh GTPRas-related protein Rab-5A / 0.710
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.710
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.708
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.707
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.705
1wdt GTPElongation factor G (EF-G-2) / 0.705
2j5x GSPADP-ribosylation factor 6 / 0.705
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.704
4x8o AP5Adenylate kinase / 0.703
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.700
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.698
4mit GTPRho-related protein racC / 0.698
5dac AGSUncharacterized protein / 0.698
1svl ADPLarge T antigen 3.6.4 0.695
2iut AGSDNA translocase FtsK / 0.693
1gwn GTPRho-related GTP-binding protein RhoE / 0.691
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.690
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
2ffq GSPRas-related protein Rab-6B / 0.686
3hpr AP5Adenylate kinase / 0.686
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.686
1zbd GTPRas-related protein Rab-3A / 0.684
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.684
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.683
3a6p GTPGTP-binding nuclear protein Ran / 0.683
4ol0 GTPGTP-binding nuclear protein Ran / 0.683
3eg5 GNPCell division control protein 42 homolog / 0.682
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.682
4tv9 GTPTubulin alpha-1B chain / 0.681
2eck ADPAdenylate kinase / 0.680
4xoi GTPTransforming protein RhoA / 0.680
4d0l GSPRas-related protein Rab-11A / 0.679
1t91 GTPRas-related protein Rab-7a / 0.677
2c5l GTPGTPase HRas / 0.677
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.677
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.677
4brd ANPEctonucleoside triphosphate diphosphohydrolase I / 0.677
3orl AGSSerine/threonine protein kinase / 0.676
5itz GTPTubulin alpha-1B chain / 0.676
3rye UNRFarnesyl pyrophosphate synthase 2.5.1.10 0.675
5d3q GDPDynamin-1 3.6.5.5 0.674
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.673
1svw GTPProbable GTP-binding protein EngB / 0.672
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.672
2y6p CTP3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 0.671
3w3z GTPGTP-binding nuclear protein Ran / 0.671
2vp0 TTPDeoxynucleoside kinase / 0.670
4dvg GSPRho family GTPase / 0.670
4dxa GSPRas-related protein Rap-1b / 0.669
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.668
3ryh GTPTubulin alpha chain / 0.667
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.666
4brg GNPEctonucleoside triphosphate diphosphohydrolase I / 0.666
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.665
3tkl GTPRas-related protein Rab-1A / 0.665
4kvg GTPRas-related protein Rap-1A / 0.665
4q23 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.664
4hse ADPChaperone protein ClpB / 0.663
1xp8 AGSProtein RecA / 0.662
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.662
2cls GTPRho-related GTP-binding protein Rho6 / 0.661
3ar4 ATPSarcoplasmic/endoplasmic reticulum calcium ATPase 1 3.6.3.8 0.661
5c46 GSPRas-related protein Rab-11A / 0.661
5la6 GTPTubulin alpha-1B chain / 0.661
3bc1 GNPRas-related protein Rab-27A / 0.658
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.656
1xts GTPGTP-binding protein Rheb / 0.656
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.656
2a84 ATPPantothenate synthetase 6.3.2.1 0.656
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.656
1a2b GSPTransforming protein RhoA / 0.655
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.655
3ref GDPRho family GTPase / 0.655
4cnz ADPNitrogen regulatory protein P-II 1 / 0.655
4nyi GNPGTPase HRas / 0.655
2fg5 GNPRas-related protein Rab-31 / 0.654
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.653
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.653
4zol GTPTubulin alpha-1B chain / 0.653
5bsm ATP4-coumarate--CoA ligase 2 6.2.1.12 0.653
1w7i ADPUnconventional myosin-Va / 0.652
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.651
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.651
4dso GSPGTPase KRas / 0.651
1xjk DGTVitamin B12-dependent ribonucleotide reductase / 0.650
4o25 GTPGTP-binding protein Rheb / 0.650