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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
2qaj AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2qaj AP5Adenylate kinase / 1.882
2eu8 AP5Adenylate kinase / 1.834
4mkg AP5Adenylate kinase / 1.689
2oo7 AP5Adenylate kinase / 1.682
3dkv AP5Adenylate kinase / 1.589
2osb AP5Adenylate kinase / 1.583
4mkf AP5Adenylate kinase / 1.430
3dl0 AP5Adenylate kinase / 1.413
4nu0 AP5Adenylate kinase / 1.370
4w5j AP5Adenylate kinase / 1.337
2aky AP5Adenylate kinase / 1.238
1p3j AP5Adenylate kinase / 1.222
4qbf AP5Adenylate kinase / 1.173
1s3g AP5Adenylate kinase / 1.075
1zio AP5Adenylate kinase / 1.065
3aky AP5Adenylate kinase / 1.055
4tyq AP5Adenylate kinase / 1.054
2rgx AP5Adenylate kinase / 0.981
4typ AP5Adenylate kinase / 0.978
4mkh AP5Adenylate kinase / 0.967
4qbh AP5Adenylate kinase / 0.937
4qbi AP5Adenylate kinase / 0.893
4jl8 ADPAdenylate kinase / 0.825
4jlo ADPAdenylate kinase / 0.825
4jld ADPAdenylate kinase / 0.799
4jky ADPAdenylate kinase / 0.796
4jl6 ADPAdenylate kinase / 0.792
4jl5 ADPAdenylate kinase / 0.791
4ike ADPAdenylate kinase / 0.790
4qbg AP5Adenylate kinase / 0.790
4jlb ADPAdenylate kinase / 0.785
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.773
1svm ATPLarge T antigen 3.6.4 0.751
4x8l AP5Adenylate kinase / 0.750
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.748
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.747
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.746
1cxz GSPTransforming protein RhoA / 0.743
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.741
2eck ADPAdenylate kinase / 0.740
3wyf GTPGTP-binding nuclear protein / 0.739
4jlp ADPAdenylate kinase / 0.739
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.734
2ffq GSPRas-related protein Rab-6B / 0.734
1gwn GTPRho-related GTP-binding protein RhoE / 0.733
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.733
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.733
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.731
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.728
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.728
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.728
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.728
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.728
1a2b GSPTransforming protein RhoA / 0.726
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.725
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.723
4ohx ADPProtein clpf-1 / 0.721
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.721
4dso GSPGTPase KRas / 0.719
4qnr ATPPsp operon transcriptional activator / 0.719
2hld ANPATP synthase subunit alpha, mitochondrial / 0.718
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.718
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.717
3eg5 GNPCell division control protein 42 homolog / 0.716
4dvg GSPRho family GTPase / 0.714
3law GNPRas-related protein Rab-7a / 0.711
5d3q GDPDynamin-1 3.6.5.5 0.708
1ake AP5Adenylate kinase / 0.706
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.705
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.705
1sxj AGSReplication factor C subunit 1 / 0.704
4v02 ATPSite-determining protein / 0.703
1l8q ADPChromosomal replication initiator protein DnaA / 0.702
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.701
3l8y GNPGTPase HRas / 0.701
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.699
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.698
2iut AGSDNA translocase FtsK / 0.697
4epx GDPGTPase KRas / 0.696
3x1w GDPRas-related protein Rap-1b / 0.695
2gcp GSPRho-related GTP-binding protein RhoC / 0.694
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.694
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.692
4mit GTPRho-related protein racC / 0.691
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.689
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.689
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.687
3k3b ADPKinesin-like protein KIF11 / 0.687
2r9v ATPATP synthase subunit alpha / 0.686
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.685
4ol0 GTPGTP-binding nuclear protein Ran / 0.685
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.684
3hpq AP5Adenylate kinase / 0.684
4oi2 ADPProtein clpf-1 / 0.684
2uyi ADPKinesin-like protein KIF11 / 0.683
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.682
2x7e ADPKinesin-like protein KIF11 / 0.682
4tq9 GDPGTPase KRas / 0.682
4yj2 GTPTubulin alpha-1B chain / 0.682
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.681
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
1oe0 TTPDeoxynucleoside kinase / 0.681
2xsz ATPRuvB-like 2 3.6.4.12 0.681
2bbw GP5Adenylate kinase 4, mitochondrial / 0.680
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.680
1e4v AP5Adenylate kinase / 0.678
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.678
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.677
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.677
3orl AGSSerine/threonine protein kinase / 0.677
4dzz ADPPlasmid partitioning protein ParF / 0.677
4zca ADPKinesin-like protein KIF11 / 0.677
1yrs ADPKinesin-like protein KIF11 / 0.675
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.675
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.674
2zr9 DTPProtein RecA / 0.673
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.672
1z6t ADPApoptotic protease-activating factor 1 / 0.672
1k5d GNPGTP-binding nuclear protein Ran / 0.670
1svl ADPLarge T antigen 3.6.4 0.670
4d0l GSPRas-related protein Rab-11A / 0.670
3m0e ATPTranscriptional regulator (NtrC family) / 0.669
1xts GTPGTP-binding protein Rheb / 0.667
2g1q ADPKinesin-like protein KIF11 / 0.667
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.667
1uad GNPRas-related protein Ral-A / 0.665
2vp0 TTPDeoxynucleoside kinase / 0.664
3vth APCCarbamoyltransferase / 0.664
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.663
1rrg GDPADP-ribosylation factor 1 / 0.663
3ryh GTPTubulin alpha chain / 0.663
3a5m ATPMajor actin / 0.662
3bc1 GNPRas-related protein Rab-27A / 0.662
3r9i ADPSeptum site-determining protein MinD / 0.662
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.662
4hse ADPChaperone protein ClpB / 0.662
4fvq ATPTyrosine-protein kinase JAK2 / 0.661
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.660
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
4rpg GDUUDP-galactopyranose mutase 5.4.99.9 0.660
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.659
4hi0 GDPUrease accessory protein UreG / 0.659
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.659
1xs4 DCPdCTP deaminase / 0.658
2o8b ADPDNA mismatch repair protein Msh2 / 0.658
5c46 GSPRas-related protein Rab-11A / 0.658
2a84 ATPPantothenate synthetase 6.3.2.1 0.657
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.657
1fnn ADPORC1-type DNA replication protein / 0.656
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
4fvr ATPTyrosine-protein kinase JAK2 / 0.656
4o25 GTPGTP-binding protein Rheb / 0.655
4to3 DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.655
3mjh GTPRas-related protein Rab-5A / 0.654
3sl2 ATPSensor histidine kinase WalK / 0.654
5la6 GTPTubulin alpha-1B chain / 0.653
1t91 GTPRas-related protein Rab-7a / 0.652
1w5s ADPORC1-type DNA replication protein 2 / 0.652
1zbd GTPRas-related protein Rab-3A / 0.652
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.652
1ii6 ADPKinesin-like protein KIF11 / 0.651
2vp2 DGTDeoxynucleoside kinase / 0.651
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
4qxa GTPRas-related protein Rab-9A / 0.651
1xjj DGTVitamin B12-dependent ribonucleotide reductase / 0.650
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.650
4ihq ADPConserved Archaeal protein / 0.650
4y0v GDPADP-ribosylation factor 1, putative / 0.650
4ylg GDPADP-ribosylation factor 1, putative / 0.650