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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
4qbh AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4qbh AP5Adenylate kinase / 1.854
4qbi AP5Adenylate kinase / 1.533
1s3g AP5Adenylate kinase / 1.129
2eu8 AP5Adenylate kinase / 1.099
4x8o AP5Adenylate kinase / 1.099
4mkf AP5Adenylate kinase / 1.095
3aky AP5Adenylate kinase / 1.083
2oo7 AP5Adenylate kinase / 1.081
1p3j AP5Adenylate kinase / 1.079
4nu0 AP5Adenylate kinase / 1.068
3dl0 AP5Adenylate kinase / 1.047
1ake AP5Adenylate kinase / 1.005
2rgx AP5Adenylate kinase / 0.984
4w5j AP5Adenylate kinase / 0.981
1e4v AP5Adenylate kinase / 0.980
2osb AP5Adenylate kinase / 0.975
4mkh AP5Adenylate kinase / 0.939
2qaj AP5Adenylate kinase / 0.937
4jl8 ADPAdenylate kinase / 0.933
3hpr AP5Adenylate kinase / 0.927
3hpq AP5Adenylate kinase / 0.915
4mkg AP5Adenylate kinase / 0.904
4ike ADPAdenylate kinase / 0.900
4jlo ADPAdenylate kinase / 0.893
1zio AP5Adenylate kinase / 0.892
4x8l AP5Adenylate kinase / 0.892
2eck ADPAdenylate kinase / 0.891
4jl5 ADPAdenylate kinase / 0.884
4jky ADPAdenylate kinase / 0.879
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.875
4qbf AP5Adenylate kinase / 0.875
4jld ADPAdenylate kinase / 0.869
4tyq AP5Adenylate kinase / 0.838
4qbg AP5Adenylate kinase / 0.836
3dkv AP5Adenylate kinase / 0.828
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.820
4jlp ADPAdenylate kinase / 0.819
2c9o ADPRuvB-like 1 3.6.4.12 0.806
1z0a GDPRas-related protein Rab-2A / 0.781
4typ AP5Adenylate kinase / 0.780
4jla ADPAdenylate kinase / 0.777
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.766
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.765
4o2r GDPGTP-binding protein Rheb / 0.765
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.764
4pk4 ADPUnconventional myosin-VI / 0.764
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.763
4hse ADPChaperone protein ClpB / 0.762
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.761
4q03 GDPGTPase KRas / 0.752
1a2b GSPTransforming protein RhoA / 0.751
5fl3 ADPPili retraction protein PilT / 0.746
4d81 ADPAAA ATPase, central domain protein / 0.743
2ql6 ADPNicotinamide riboside kinase 1 / 0.739
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.738
3q5d GDPAtlastin-1 3.6.5 0.737
2aky AP5Adenylate kinase / 0.736
3l9h ADPKinesin-like protein KIF11 / 0.736
1cxz GSPTransforming protein RhoA / 0.735
4jlb ADPAdenylate kinase / 0.735
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.734
2xsz ATPRuvB-like 2 3.6.4.12 0.733
3tqc ADPPantothenate kinase / 0.732
2bbw GP5Adenylate kinase 4, mitochondrial / 0.730
1m7b GTPRho-related GTP-binding protein RhoE / 0.729
4ww4 ADPRuvB-like helicase / 0.726
4cym GCPRas-related protein Rab-32 / 0.723
3d8b ADPFidgetin-like protein 1 3.6.4 0.722
4o2l GTPGTP-binding protein Rheb / 0.722
3ea5 GDPGTP-binding nuclear protein Ran / 0.720
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.715
4jsy GTPMetallophosphoesterase / 0.711
2q2z ADPKinesin-like protein KIF11 / 0.710
5d3q GDPDynamin-1 3.6.5.5 0.710
4lhv GDPRas-related protein Rab-8A / 0.707
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.703
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.698
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.698
3b1x GNPFerrous iron transport protein B / 0.696
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.696
1ny5 ADPTranscriptional regulator (NtrC family) / 0.695
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.695
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.695
1sq5 ADPPantothenate kinase 2.7.1.33 0.691
4l9s GDPGTPase HRas / 0.689
2gil GTPRas-related protein Rab-6A / 0.688
3k1j ADPATP-dependent protease Lon / 0.688
3r9i ADPSeptum site-determining protein MinD / 0.688
3tlx ADPAdenylate kinase 2 / 0.688
5fm6 ADPRuvB-like helicase / 0.688
1w7i ADPUnconventional myosin-Va / 0.685
2dr3 ADPUPF0273 protein PH0284 / 0.684
2zts ADPUncharacterized protein / 0.682
2vf7 ADPUvrABC system protein A / 0.681
5bn4 ANPV-type ATP synthase alpha chain / 0.678
2j9l ATPH(+)/Cl(-) exchange transporter 5 / 0.676
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.676
2ffq GSPRas-related protein Rab-6B / 0.675
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.675
3kkq GDPRas-related protein M-Ras / 0.675
3tnf GNPRas-related protein Rab-8A / 0.675
3oee ANPATP synthase subunit alpha, mitochondrial / 0.674
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.674
4yqf GDPSeptin-9 / 0.674
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.672
4pjk ADPMyosin-2 heavy chain / 0.672
4nh0 ATPESX secretion system protein EccC / 0.671
1d5c GDPGTPase (Rab6) / 0.670
2d4h 5GPGuanylate-binding protein 1 / 0.669
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.669
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.669
3bxz ADPProtein translocase subunit SecA / 0.668
2j9g ADPBiotin carboxylase 6.3.4.14 0.667
4ncl GDPEukaryotic translation initiation factor 5B / 0.666
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.663
3tw6 ADPPyruvate carboxylase / 0.663
4c2u ANPDNA helicase / 0.662
3kz1 GSPTransforming protein RhoA / 0.661
3qfs NAPNADPH--cytochrome P450 reductase / 0.660
1g6o ADPCag alpha / 0.659
3kuc GDPRas-related protein Rap-1A / 0.659
4c30 ANPDNA helicase / 0.657
2iut AGSDNA translocase FtsK / 0.656
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.656
5i4n ATPTyrosine-protein kinase JAK2 / 0.654
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.653
4rz3 ADPSite-determining protein / 0.653
2e91 ZOLGeranylgeranyl pyrophosphate synthase / 0.652
2gcp GSPRho-related GTP-binding protein RhoC / 0.651
3qft NAPNADPH--cytochrome P450 reductase / 0.651
4e07 ACPPlasmid partitioning protein ParF / 0.651
2x0q ATPAlcaligin biosynthesis protein / 0.650
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.650
3lbi GNPGTPase HRas / 0.650
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.650
3ref GDPRho family GTPase / 0.650
4d0l GSPRas-related protein Rab-11A / 0.650