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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
1e4v AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1e4v AP5Adenylate kinase / 1.921
4x8o AP5Adenylate kinase / 1.272
3hpr AP5Adenylate kinase / 1.197
4x8l AP5Adenylate kinase / 1.144
3hpq AP5Adenylate kinase / 1.106
1ake AP5Adenylate kinase / 1.060
2rgx AP5Adenylate kinase / 1.028
4qbh AP5Adenylate kinase / 0.980
1s3g AP5Adenylate kinase / 0.977
4mkf AP5Adenylate kinase / 0.945
4qbf AP5Adenylate kinase / 0.894
4jl5 ADPAdenylate kinase / 0.862
4jl6 ADPAdenylate kinase / 0.855
4qbg AP5Adenylate kinase / 0.854
4jlo ADPAdenylate kinase / 0.852
4w5j AP5Adenylate kinase / 0.849
4cf7 ADPAdenylate kinase / 0.847
2oo7 AP5Adenylate kinase / 0.834
2eck ADPAdenylate kinase / 0.833
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.830
4ike ADPAdenylate kinase / 0.819
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.816
4jld ADPAdenylate kinase / 0.812
1zio AP5Adenylate kinase / 0.808
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.807
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.799
1d5c GDPGTPase (Rab6) / 0.798
4jl8 ADPAdenylate kinase / 0.797
4qbi AP5Adenylate kinase / 0.794
4mkh AP5Adenylate kinase / 0.793
4o25 GTPGTP-binding protein Rheb / 0.791
4jky ADPAdenylate kinase / 0.789
3m0e ATPTranscriptional regulator (NtrC family) / 0.785
1z2a GDPRas-related protein Rab-23 / 0.784
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.782
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.781
2ffq GSPRas-related protein Rab-6B / 0.781
3dl0 AP5Adenylate kinase / 0.781
1cxz GSPTransforming protein RhoA / 0.780
2ql6 ADPNicotinamide riboside kinase 1 / 0.780
4dxa GSPRas-related protein Rap-1b / 0.779
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.776
3dkv AP5Adenylate kinase / 0.776
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.774
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.773
4nu0 AP5Adenylate kinase / 0.773
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.767
4mkg AP5Adenylate kinase / 0.767
2fe4 GDPRas-related protein Rab-6B / 0.766
4ql3 GDPGTPase KRas / 0.765
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.764
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.762
1ow3 GDPTransforming protein RhoA / 0.757
2c96 ATPPsp operon transcriptional activator / 0.757
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.755
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.752
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.751
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.751
5c46 GSPRas-related protein Rab-11A / 0.748
4kvg GTPRas-related protein Rap-1A / 0.747
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.746
3kud GDPGTPase HRas / 0.746
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.745
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.745
4q03 GDPGTPase KRas / 0.745
4ihq ADPConserved Archaeal protein / 0.743
2gil GTPRas-related protein Rab-6A / 0.741
4jlp ADPAdenylate kinase / 0.738
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.735
1dvr ATFAdenylate kinase / 0.733
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.733
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.733
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.733
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.733
1sq5 ADPPantothenate kinase 2.7.1.33 0.731
3tqc ADPPantothenate kinase / 0.731
1t91 GTPRas-related protein Rab-7a / 0.729
3zia ATPATP synthase subunit alpha, mitochondrial / 0.729
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.726
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.726
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.726
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.724
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.723
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.723
1ii6 ADPKinesin-like protein KIF11 / 0.723
2c5l GTPGTPase HRas / 0.723
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.722
4asu ADPATP synthase subunit alpha, mitochondrial / 0.722
2qen ADPWalker-Type ATPase / 0.721
4d0l GSPRas-related protein Rab-11A / 0.721
4tyq AP5Adenylate kinase / 0.720
2x7e ADPKinesin-like protein KIF11 / 0.717
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.714
2vf7 ADPUvrABC system protein A / 0.714
3d8b ADPFidgetin-like protein 1 3.6.4 0.713
4v02 ATPSite-determining protein / 0.710
2fg5 GNPRas-related protein Rab-31 / 0.707
4ys0 ADPProtein translocase subunit SecA / 0.707
2y65 ADPKinesin heavy chain / 0.705
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.705
3aky AP5Adenylate kinase / 0.704
3vhx GTPADP-ribosylation factor 6 / 0.703
4gp6 ADPMetallophosphoesterase / 0.703
3tlx ADPAdenylate kinase 2 / 0.702
4ww4 ADPRuvB-like helicase / 0.701
1sdm ADPKinesin heavy chain-like protein / 0.700
2aky AP5Adenylate kinase / 0.700
1z0a GDPRas-related protein Rab-2A / 0.699
2c9o ADPRuvB-like 1 3.6.4.12 0.699
3q9l ATPSeptum site-determining protein MinD / 0.699
4ohx ADPProtein clpf-1 / 0.699
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.697
1mma ADPMyosin-2 heavy chain / 0.695
4luc GDPGTPase KRas / 0.695
1l8q ADPChromosomal replication initiator protein DnaA / 0.694
4o2r GDPGTP-binding protein Rheb / 0.691
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.690
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.689
4b7b ADPKinesin-like protein KIF11 / 0.688
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.688
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.684
2osb AP5Adenylate kinase / 0.683
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.683
3l9h ADPKinesin-like protein KIF11 / 0.682
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.682
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.681
2bbw GP5Adenylate kinase 4, mitochondrial / 0.679
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.678
2qaj AP5Adenylate kinase / 0.678
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.674
1jx2 ADPMyosin-2 heavy chain / 0.672
2hld ANPATP synthase subunit alpha, mitochondrial / 0.672
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
4pfp ADPUnconventional myosin-VI / 0.672
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.671
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
1fmw ATPMyosin-2 heavy chain / 0.670
1s1c GNPTransforming protein RhoA / 0.670
2o8b ADPDNA mismatch repair protein Msh2 / 0.669
3k3b ADPKinesin-like protein KIF11 / 0.669
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.669
2eu8 AP5Adenylate kinase / 0.668
4nh0 ATPESX secretion system protein EccC / 0.668
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.667
4pjk ADPMyosin-2 heavy chain / 0.667
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.666
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.663
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.661
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.660
4d81 ADPAAA ATPase, central domain protein / 0.660
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.660
4typ AP5Adenylate kinase / 0.660
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.659
2ilv C5PAlpha-2,3/2,6-sialyltransferase/sialidase / 0.659
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.658
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.657
4jlb ADPAdenylate kinase / 0.656
1eyy NAPNADP-dependent fatty aldehyde dehydrogenase 1.2.1.4 0.655
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.655
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
1yrs ADPKinesin-like protein KIF11 / 0.653
4dve BTNBiotin transporter BioY / 0.653
2xsz ATPRuvB-like 2 3.6.4.12 0.652
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.651
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
2zts ADPUncharacterized protein / 0.651
3uk6 ADPRuvB-like 2 3.6.4.12 0.650