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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
2rgx AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2rgx AP5Adenylate kinase / 1.616
1p3j AP5Adenylate kinase / 1.107
2eu8 AP5Adenylate kinase / 1.064
4mkh AP5Adenylate kinase / 1.060
4x8l AP5Adenylate kinase / 1.059
4mkf AP5Adenylate kinase / 1.057
4mkg AP5Adenylate kinase / 1.054
3dl0 AP5Adenylate kinase / 1.050
1e4v AP5Adenylate kinase / 1.028
1zio AP5Adenylate kinase / 1.021
2aky AP5Adenylate kinase / 1.017
4x8o AP5Adenylate kinase / 1.012
2oo7 AP5Adenylate kinase / 1.000
4qbh AP5Adenylate kinase / 0.984
4w5j AP5Adenylate kinase / 0.984
2qaj AP5Adenylate kinase / 0.981
2osb AP5Adenylate kinase / 0.976
4jl6 ADPAdenylate kinase / 0.969
4qbg AP5Adenylate kinase / 0.950
4tyq AP5Adenylate kinase / 0.934
4jky ADPAdenylate kinase / 0.930
3dkv AP5Adenylate kinase / 0.925
4cf7 ADPAdenylate kinase / 0.914
4jld ADPAdenylate kinase / 0.893
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.891
3hpq AP5Adenylate kinase / 0.875
4jl5 ADPAdenylate kinase / 0.872
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.862
1s3g AP5Adenylate kinase / 0.856
4qm6 GTPMetallophosphoesterase / 0.856
3hpr AP5Adenylate kinase / 0.851
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.848
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.848
3tlx ADPAdenylate kinase 2 / 0.848
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.847
4jsy GTPMetallophosphoesterase / 0.840
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.830
1cxz GSPTransforming protein RhoA / 0.828
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.828
4kvg GTPRas-related protein Rap-1A / 0.827
4qbi AP5Adenylate kinase / 0.826
1ake AP5Adenylate kinase / 0.824
4gp6 ADPMetallophosphoesterase / 0.824
2fna ADPUncharacterized protein / 0.820
3mjh GTPRas-related protein Rab-5A / 0.819
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.818
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.817
5bn3 ADPV-type ATP synthase alpha chain / 0.817
5bn3 ADPNEQ263 / 0.817
2cl6 CAGGTPase HRas / 0.816
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.815
4g0n GNPGTPase HRas / 0.815
1gwn GTPRho-related GTP-binding protein RhoE / 0.811
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.804
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.804
3law GNPRas-related protein Rab-7a / 0.803
4asu ADPATP synthase subunit alpha, mitochondrial / 0.801
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.800
4pfp ADPUnconventional myosin-VI / 0.799
4pjk ADPMyosin-2 heavy chain / 0.799
1mma ADPMyosin-2 heavy chain / 0.797
3w3z GTPGTP-binding nuclear protein Ran / 0.795
3aky AP5Adenylate kinase / 0.793
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.791
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.788
4ql3 GDPGTPase KRas / 0.786
3zia ATPATP synthase subunit alpha, mitochondrial / 0.785
4c30 ANPDNA helicase / 0.785
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.783
2r9v ATPATP synthase subunit alpha / 0.782
2bku GTPGTP-binding nuclear protein Ran / 0.779
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.779
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.779
4dvg GSPRho family GTPase / 0.778
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.778
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.776
3bc1 GNPRas-related protein Rab-27A / 0.776
2gm1 ADPKinesin-like protein KIF11 / 0.775
3ftq GNPSeptin-2 / 0.773
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.772
3cob ADPKinesin heavy chain-like protein / 0.771
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.771
2ce2 GDPGTPase HRas / 0.770
3b1x GNPFerrous iron transport protein B / 0.770
2gil GTPRas-related protein Rab-6A / 0.769
4qnr ATPPsp operon transcriptional activator / 0.769
4nh0 ATPESX secretion system protein EccC / 0.768
1jx2 ADPMyosin-2 heavy chain / 0.767
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.767
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.767
4o2l GTPGTP-binding protein Rheb / 0.767
1z0f GDPRas-related protein Rab-14 / 0.766
4d0l GSPRas-related protein Rab-11A / 0.766
1ank ANPAdenylate kinase / 0.765
4ike ADPAdenylate kinase / 0.765
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.765
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.764
2ql6 ADPNicotinamide riboside kinase 1 / 0.764
2bc9 GNPGuanylate-binding protein 1 / 0.761
2cls GTPRho-related GTP-binding protein Rho6 / 0.761
4dzz ADPPlasmid partitioning protein ParF / 0.761
4yqf GDPSeptin-9 / 0.761
2ffq GSPRas-related protein Rab-6B / 0.760
2uyi ADPKinesin-like protein KIF11 / 0.759
2x7e ADPKinesin-like protein KIF11 / 0.759
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.759
2x2r ADPKinesin-like protein KIF11 / 0.758
5aun ADPIron-sulfur cluster carrier protein / 0.758
5c46 GSPRas-related protein Rab-11A / 0.758
1fnn ADPORC1-type DNA replication protein / 0.755
1oix GDPRas-related protein Rab-11A / 0.754
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.754
3ref GDPRho family GTPase / 0.754
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.753
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.752
4jlo ADPAdenylate kinase / 0.752
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.751
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.750
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.750
2eck ADPAdenylate kinase / 0.749
4ihq ADPConserved Archaeal protein / 0.749
4qos ADPPsp operon transcriptional activator / 0.749
5fl3 ADPPili retraction protein PilT / 0.749
1mmg AGSMyosin-2 heavy chain / 0.747
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.747
2y65 ADPKinesin heavy chain / 0.747
4qbf AP5Adenylate kinase / 0.747
3q5d GDPAtlastin-1 3.6.5 0.746
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.745
4js0 GNPCell division control protein 42 homolog / 0.745
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.744
2pg2 ADPKinesin-like protein KIF11 / 0.744
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.744
4o2r GDPGTP-binding protein Rheb / 0.744
1w5t ADPORC1-type DNA replication protein 2 / 0.742
4nu0 AP5Adenylate kinase / 0.742
4hse ADPChaperone protein ClpB / 0.741
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.741
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.739
2gcp GSPRho-related GTP-binding protein RhoC / 0.738
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.738
4zca ADPKinesin-like protein KIF11 / 0.738
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.736
5dha GNPGTP-binding nuclear protein Ran / 0.734
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.733
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.733
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.733
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.732
2zr9 DTPProtein RecA / 0.731
2xae ADPKinesin-like protein KIF11 / 0.730
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.730
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.728
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.727
4dxa GSPRas-related protein Rap-1b / 0.727
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.726
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.726
2bbw GP5Adenylate kinase 4, mitochondrial / 0.725
3wyf GTPGTP-binding nuclear protein / 0.725
5cyo GDPSeptin-9 / 0.724
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.723
1b7t ADPMyosin heavy chain, striated muscle / 0.722
1ii6 ADPKinesin-like protein KIF11 / 0.721
2c96 ATPPsp operon transcriptional activator / 0.721
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.720
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.719
2l0x GDPGTP-binding protein Rheb / 0.719
4b7b ADPKinesin-like protein KIF11 / 0.719
4itr GDPCell division control protein 42 homolog / 0.719
1mab ATPATP synthase subunit alpha, mitochondrial / 0.717
1yrs ADPKinesin-like protein KIF11 / 0.717
3k3b ADPKinesin-like protein KIF11 / 0.715
4a1z ADPKinesin-like protein KIF11 / 0.715
1ny5 ADPTranscriptional regulator (NtrC family) / 0.712
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.712
4lhv GDPRas-related protein Rab-8A / 0.711
1e4y AP5Adenylate kinase / 0.710
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.709
5dac AGSUncharacterized protein / 0.708
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.707
2vp0 TTPDeoxynucleoside kinase / 0.707
4v02 ATPSite-determining protein / 0.706
1l8q ADPChromosomal replication initiator protein DnaA / 0.705
5fm6 ADPRuvB-like helicase / 0.705
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.703
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.703
4pk4 ADPUnconventional myosin-VI / 0.703
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.701
1fmw ATPMyosin-2 heavy chain / 0.700
1oe0 TTPDeoxynucleoside kinase / 0.700
1svl ADPLarge T antigen 3.6.4 0.700
2jlr ANPGenome polyprotein 3.4.21.91 0.700
3tqc ADPPantothenate kinase / 0.699
4typ AP5Adenylate kinase / 0.699
2g1q ADPKinesin-like protein KIF11 / 0.698
1dvr ATFAdenylate kinase / 0.697
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.697
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.697
4db1 ANPMyosin-7 / 0.697
2iut AGSDNA translocase FtsK / 0.695
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.695
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.694
3thy ADPDNA mismatch repair protein Msh2 / 0.694
1m7b GTPRho-related GTP-binding protein RhoE / 0.692
3tkl GTPRas-related protein Rab-1A / 0.692
5bn4 ANPV-type ATP synthase alpha chain / 0.692
2c9o ADPRuvB-like 1 3.6.4.12 0.691
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.690
2xul ATPNitrogen regulatory protein P-II / 0.690
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.689
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
3nbx ADPATPase RavA 3.6.3 0.689
1a2b GSPTransforming protein RhoA / 0.687
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.686
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.685
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.685
4c2u ANPDNA helicase / 0.685
1z0a GDPRas-related protein Rab-2A / 0.684
2xsz ATPRuvB-like 2 3.6.4.12 0.684
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.684
4ww4 ADPRuvB-like helicase / 0.683
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.682
3tjz GNPADP-ribosylation factor 1 / 0.682
1sxj AGSReplication factor C subunit 1 / 0.681
3c41 ANPAmino acid ABC transporter / 0.681
4o3m ADPBloom syndrome protein 3.6.4.12 0.681
2c5l GTPGTPase HRas / 0.680
1p52 ADPArginine kinase 2.7.3.3 0.678
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.678
1xts GTPGTP-binding protein Rheb / 0.678
3pcr GTPADP-ribosylation factor 6 / 0.678
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.675
2fl2 ADPKinesin-like protein KIF11 / 0.675
2zet GTPRas-related protein Rab-27B / 0.675
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.673
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.673
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.671
3kz1 GSPTransforming protein RhoA / 0.670
2dft ADPShikimate kinase 2.7.1.71 0.669
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.669
5fv0 ONAESX secretion system protein EccC / 0.669
1w7i ADPUnconventional myosin-Va / 0.668
4dso GSPGTPase KRas / 0.668
4i1v ADPDephospho-CoA kinase / 0.668
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.668
1wdt GTPElongation factor G (EF-G-2) / 0.667
4ol0 GTPGTP-binding nuclear protein Ran / 0.667
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.667
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.666
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.666
3k1j ADPATP-dependent protease Lon / 0.665
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.664
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.664
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.663
4fvq ATPTyrosine-protein kinase JAK2 / 0.663
4ihj GTPTubulin alpha-1B chain / 0.663
4o25 GTPGTP-binding protein Rheb / 0.663
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.663
4wbn GTPTubulin alpha-1B chain / 0.663
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.662
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
4fvr ATPTyrosine-protein kinase JAK2 / 0.662
5la6 GTPTubulin alpha-1B chain / 0.662
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.661
1z2c GNPRho-related GTP-binding protein RhoC / 0.661
4l16 ADPFidgetin-like protein 1 3.6.4 0.661
1g17 GNPRas-related protein SEC4 / 0.660
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.660
4dfk 0L5DNA polymerase I, thermostable 2.7.7.7 0.659
3aez GDPPantothenate kinase 2.7.1.33 0.658
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.657
1hck ATPCyclin-dependent kinase 2 2.7.11.22 0.657
2zsa ADPPantothenate kinase 2.7.1.33 0.657
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.657
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.656
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.655
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.655
3bbp GTPRas-related protein Rab-6A / 0.655
3mhy ATPNitrogen regulatory protein P-II 1 / 0.655
2a5y ATPCell death protein 4 / 0.654
3ryh GTPTubulin alpha chain / 0.654
4xoi GTPTransforming protein RhoA / 0.654
4cok TPPPyruvate decarboxylase / 0.653
3g6x DGTDNA polymerase iota 2.7.7.7 0.652
3m0e ATPTranscriptional regulator (NtrC family) / 0.652
4qxa GTPRas-related protein Rab-9A / 0.652
5b2z GNPGTPase HRas / 0.651
1p4m ADPRiboflavin kinase 2.7.1.26 0.650
3pit GNPRas-related protein M-Ras / 0.650
3rsl GNPGTPase HRas / 0.650
4dlv GNPGTPase HRas / 0.650
4uj3 GNPRas-related protein Rab-11A / 0.650