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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
1e4y AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1e4y AP5Adenylate kinase / 1.695
3hpq AP5Adenylate kinase / 0.936
3hpr AP5Adenylate kinase / 0.905
4qbi AP5Adenylate kinase / 0.854
4jlb ADPAdenylate kinase / 0.840
4x8l AP5Adenylate kinase / 0.816
4jl8 ADPAdenylate kinase / 0.815
1a2b GSPTransforming protein RhoA / 0.795
4qm6 GTPMetallophosphoesterase / 0.787
4x8o AP5Adenylate kinase / 0.786
4dso GSPGTPase KRas / 0.777
4ike ADPAdenylate kinase / 0.777
4ww4 ADPRuvB-like helicase / 0.775
1ake AP5Adenylate kinase / 0.772
4jlo ADPAdenylate kinase / 0.771
3tlx ADPAdenylate kinase 2 / 0.770
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.759
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.759
3mjh GTPRas-related protein Rab-5A / 0.759
4jky ADPAdenylate kinase / 0.759
2eck ADPAdenylate kinase / 0.756
4dxa GSPRas-related protein Rap-1b / 0.753
1d5c GDPGTPase (Rab6) / 0.750
1cxz GSPTransforming protein RhoA / 0.746
4kvg GTPRas-related protein Rap-1A / 0.745
1z0d GDPRas-related protein Rab-5C / 0.743
4pfp ADPUnconventional myosin-VI / 0.743
4yqf GDPSeptin-9 / 0.743
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.742
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.742
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.739
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.737
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.737
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.737
2dft ADPShikimate kinase 2.7.1.71 0.734
2gm1 ADPKinesin-like protein KIF11 / 0.733
3r9i ADPSeptum site-determining protein MinD / 0.731
1z6t ADPApoptotic protease-activating factor 1 / 0.730
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.729
1mma ADPMyosin-2 heavy chain / 0.728
1t91 GTPRas-related protein Rab-7a / 0.727
4l8g GDPGTPase KRas / 0.727
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.726
1s3g AP5Adenylate kinase / 0.726
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.726
4pk4 ADPUnconventional myosin-VI / 0.725
1g16 GDPRas-related protein SEC4 / 0.724
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.724
2gil GTPRas-related protein Rab-6A / 0.723
5ftc ADPTPR domain protein / 0.722
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.720
4jl5 ADPAdenylate kinase / 0.720
4d0l GSPRas-related protein Rab-11A / 0.717
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.716
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.715
4epw GDPGTPase KRas / 0.715
3kuc GDPRas-related protein Rap-1A / 0.714
3zia ATPATP synthase subunit alpha, mitochondrial / 0.714
4jld ADPAdenylate kinase / 0.714
1jx2 ADPMyosin-2 heavy chain / 0.713
1ow3 GDPTransforming protein RhoA / 0.713
4jl6 ADPAdenylate kinase / 0.713
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.713
1z0a GDPRas-related protein Rab-2A / 0.712
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.711
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.711
2rgx AP5Adenylate kinase / 0.710
4tq9 GDPGTPase KRas / 0.710
1xmv ADPProtein RecA / 0.709
4jsy GTPMetallophosphoesterase / 0.709
4o25 GTPGTP-binding protein Rheb / 0.709
1ny5 ADPTranscriptional regulator (NtrC family) / 0.707
1w5t ADPORC1-type DNA replication protein 2 / 0.706
2eu8 AP5Adenylate kinase / 0.706
2qen ADPWalker-Type ATPase / 0.704
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.703
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.703
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.702
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.702
1xts GTPGTP-binding protein Rheb / 0.701
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.701
5fm6 ADPRuvB-like helicase / 0.701
3kkq GDPRas-related protein M-Ras / 0.700
4iei ADPGene 2 protein / 0.700
1wa5 GTPGTP-binding nuclear protein Ran / 0.699
2fe4 GDPRas-related protein Rab-6B / 0.698
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.698
4q03 GDPGTPase KRas / 0.698
1yrs ADPKinesin-like protein KIF11 / 0.696
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.696
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.696
4b7b ADPKinesin-like protein KIF11 / 0.696
4lpk GDPGTPase KRas / 0.696
1sdm ADPKinesin heavy chain-like protein / 0.695
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.695
4oi2 ADPProtein clpf-1 / 0.695
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.694
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.694
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.694
4ihq ADPConserved Archaeal protein / 0.693
4v02 ATPSite-determining protein / 0.693
2aky AP5Adenylate kinase / 0.692
2fna ADPUncharacterized protein / 0.692
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.692
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.691
4dzz ADPPlasmid partitioning protein ParF / 0.691
2cl6 CAGGTPase HRas / 0.690
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.690
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.689
2oo7 AP5Adenylate kinase / 0.689
5d3q GDPDynamin-1 3.6.5.5 0.689
4hse ADPChaperone protein ClpB / 0.688
4xoi GTPTransforming protein RhoA / 0.688
2g1q ADPKinesin-like protein KIF11 / 0.687
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.687
3k1j ADPATP-dependent protease Lon / 0.687
4obe GDPGTPase KRas / 0.687
4ldj GDPGTPase KRas / 0.686
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.685
1l8q ADPChromosomal replication initiator protein DnaA / 0.685
4dvg GSPRho family GTPase / 0.685
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.683
3w3z GTPGTP-binding nuclear protein Ran / 0.682
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.681
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.681
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.680
3thy ADPDNA mismatch repair protein Msh2 / 0.680
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.680
2ffq GSPRas-related protein Rab-6B / 0.679
4tyq AP5Adenylate kinase / 0.679
3t1t GDPProbable gliding protein mglA / 0.678
5k5z ANPUncharacterized protein / 0.678
3uk6 ADPRuvB-like 2 3.6.4.12 0.677
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.676
3ieu GDPGTPase Era / 0.676
4jla ADPAdenylate kinase / 0.676
3nbz GTPGTP-binding nuclear protein Ran / 0.674
4xsg GSPTransforming protein RhoA / 0.673
2ad5 ADPCTP synthase / 0.672
3bbp GTPRas-related protein Rab-6A / 0.671
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.671
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.670
4a51 ADPKinesin-like protein KIF11 / 0.670
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.669
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.668
4qbg AP5Adenylate kinase / 0.668
5aun ADPIron-sulfur cluster carrier protein / 0.668
2c96 ATPPsp operon transcriptional activator / 0.666
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.666
4gp6 ADPMetallophosphoesterase / 0.665
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.665
3q5d GDPAtlastin-1 3.6.5 0.664
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.662
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.661
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.661
1m7b GTPRho-related GTP-binding protein RhoE / 0.661
4mit GTPRho-related protein racC / 0.661
2ql6 ADPNicotinamide riboside kinase 1 / 0.660
2x7e ADPKinesin-like protein KIF11 / 0.659
4o2r GDPGTP-binding protein Rheb / 0.659
4xvu ATPATPase GET3 / 0.659
3aky AP5Adenylate kinase / 0.658
3dl0 AP5Adenylate kinase / 0.658
4pjk ADPMyosin-2 heavy chain / 0.656
1zw5 ZOLFarnesyl pyrophosphate synthase 2.5.1.10 0.655
1zio AP5Adenylate kinase / 0.654
4cym GCPRas-related protein Rab-32 / 0.654
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.654
4d81 ADPAAA ATPase, central domain protein / 0.653
3tw6 ADPPyruvate carboxylase / 0.652
1z2c GNPRho-related GTP-binding protein RhoC / 0.650