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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
4qbi AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4qbi AP5Adenylate kinase / 1.767
4qbh AP5Adenylate kinase / 1.533
4mkg AP5Adenylate kinase / 1.037
3aky AP5Adenylate kinase / 1.009
4mkf AP5Adenylate kinase / 0.980
2eu8 AP5Adenylate kinase / 0.968
4cf7 ADPAdenylate kinase / 0.956
4jl5 ADPAdenylate kinase / 0.908
3dl0 AP5Adenylate kinase / 0.905
2oo7 AP5Adenylate kinase / 0.901
1ank ANPAdenylate kinase / 0.899
4jky ADPAdenylate kinase / 0.899
4mkh AP5Adenylate kinase / 0.897
2qaj AP5Adenylate kinase / 0.893
4jlo ADPAdenylate kinase / 0.889
4jl6 ADPAdenylate kinase / 0.875
1p3j AP5Adenylate kinase / 0.871
1ake AP5Adenylate kinase / 0.866
4ike ADPAdenylate kinase / 0.862
1e4y AP5Adenylate kinase / 0.854
2eck ADPAdenylate kinase / 0.853
4x8l AP5Adenylate kinase / 0.852
3hpr AP5Adenylate kinase / 0.849
3dkv AP5Adenylate kinase / 0.844
4tyq AP5Adenylate kinase / 0.842
1zio AP5Adenylate kinase / 0.838
2osb AP5Adenylate kinase / 0.836
2rgx AP5Adenylate kinase / 0.826
4qbf AP5Adenylate kinase / 0.826
4jl8 ADPAdenylate kinase / 0.825
4qbg AP5Adenylate kinase / 0.823
4x8o AP5Adenylate kinase / 0.813
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.806
1e4v AP5Adenylate kinase / 0.794
4nu0 AP5Adenylate kinase / 0.791
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.788
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.780
4kvg GTPRas-related protein Rap-1A / 0.777
1mma ADPMyosin-2 heavy chain / 0.776
1mmg AGSMyosin-2 heavy chain / 0.773
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.773
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.772
3hpq AP5Adenylate kinase / 0.770
4jlb ADPAdenylate kinase / 0.769
1z2a GDPRas-related protein Rab-23 / 0.766
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.766
4pk4 ADPUnconventional myosin-VI / 0.766
2ql6 ADPNicotinamide riboside kinase 1 / 0.763
4jlp ADPAdenylate kinase / 0.762
1jx2 ADPMyosin-2 heavy chain / 0.761
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.761
2c9o ADPRuvB-like 1 3.6.4.12 0.760
4w5j AP5Adenylate kinase / 0.757
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.755
4ylg GDPADP-ribosylation factor 1, putative / 0.753
4ihq ADPConserved Archaeal protein / 0.752
4lhw GNPRas-related protein Rab-8A / 0.752
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.750
2xsz ATPRuvB-like 2 3.6.4.12 0.750
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.749
4xsg GSPTransforming protein RhoA / 0.749
4ql3 GDPGTPase KRas / 0.746
5fl3 ADPPili retraction protein PilT / 0.745
2c5l GTPGTPase HRas / 0.744
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.742
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.741
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.741
4c2u ANPDNA helicase / 0.739
4dxa GSPRas-related protein Rap-1b / 0.739
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.738
2gm1 ADPKinesin-like protein KIF11 / 0.738
3lbn GNPGTPase HRas / 0.738
4l8g GDPGTPase KRas / 0.738
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.736
3kkq GDPRas-related protein M-Ras / 0.735
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.735
4q03 GDPGTPase KRas / 0.735
4lpk GDPGTPase KRas / 0.734
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.733
2ce2 GDPGTPase HRas / 0.729
3b1x GNPFerrous iron transport protein B / 0.728
4o25 GTPGTP-binding protein Rheb / 0.726
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.723
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.723
3i3s GNPGTPase HRas / 0.722
3rs0 GNPGTPase HRas / 0.721
4cym GCPRas-related protein Rab-32 / 0.721
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.720
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.719
4d0l GSPRas-related protein Rab-11A / 0.718
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.717
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.715
3oiv GNPGTPase HRas / 0.715
1sq5 ADPPantothenate kinase 2.7.1.33 0.714
3tlx ADPAdenylate kinase 2 / 0.714
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.713
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.713
1ow3 GDPTransforming protein RhoA / 0.712
4epw GDPGTPase KRas / 0.712
4jld ADPAdenylate kinase / 0.712
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.710
4ww4 ADPRuvB-like helicase / 0.710
1xmv ADPProtein RecA / 0.709
5l3s GNPSignal recognition particle receptor FtsY / 0.709
4dlw GNPGTPase HRas / 0.708
4dzz ADPPlasmid partitioning protein ParF / 0.708
5c46 GSPRas-related protein Rab-11A / 0.708
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.707
3bc1 GNPRas-related protein Rab-27A / 0.707
1d5c GDPGTPase (Rab6) / 0.706
1zc4 GNPRas-related protein Ral-A / 0.706
3l9h ADPKinesin-like protein KIF11 / 0.705
3rs4 GNPGTPase HRas / 0.704
3rs7 GNPGTPase HRas / 0.704
3rsl GNPGTPase HRas / 0.704
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.703
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.702
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.701
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.701
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.699
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.699
1mab ATPATP synthase subunit alpha, mitochondrial / 0.697
4uj5 GNPRas-related protein Rab-11A / 0.697
1w5t ANPORC1-type DNA replication protein 2 / 0.696
1s3g AP5Adenylate kinase / 0.695
3rab GNPRas-related protein Rab-3A / 0.694
3lbi GNPGTPase HRas / 0.693
2bbw GP5Adenylate kinase 4, mitochondrial / 0.691
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.690
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.690
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.689
4yqf GDPSeptin-9 / 0.689
5d3q GDPDynamin-1 3.6.5.5 0.689
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.688
1ii6 ADPKinesin-like protein KIF11 / 0.687
3kz1 GSPTransforming protein RhoA / 0.686
4dlt GNPGTPase HRas / 0.686
1g6o ADPCag alpha / 0.685
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.685
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.685
3r9i ADPSeptum site-determining protein MinD / 0.684
4dso GSPGTPase KRas / 0.684
2aky AP5Adenylate kinase / 0.683
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.683
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.683
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.683
3law GNPRas-related protein Rab-7a / 0.682
4dlx GNPGTPase HRas / 0.682
2q2z ADPKinesin-like protein KIF11 / 0.681
3q9l ATPSeptum site-determining protein MinD / 0.681
1svl ADPLarge T antigen 3.6.4 0.678
1sxj AGSReplication factor C subunit 1 / 0.678
4xvu ATPATPase GET3 / 0.678
1z0a GDPRas-related protein Rab-2A / 0.673
3dzd ADPTranscriptional regulator (NtrC family) / 0.672
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.672
5bn4 ANPV-type ATP synthase alpha chain / 0.672
1cxz GSPTransforming protein RhoA / 0.669
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.669
2zsb ADPPantothenate kinase 2.7.1.33 0.668
3uk6 ADPRuvB-like 2 3.6.4.12 0.666
3a58 GNPGTP-binding protein RHO1 / 0.664
2ffq GSPRas-related protein Rab-6B / 0.663
2zs9 ADPPantothenate kinase 2.7.1.33 0.663
3tw6 ADPPyruvate carboxylase / 0.663
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
3oiu GNPGTPase HRas / 0.660
5cyo GDPSeptin-9 / 0.660
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.659
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.658
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.657
1nbm ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.656
2xto GDPGTPase IMAP family member 2 / 0.655
3v4f GNPGTPase HRas / 0.655
4zca ADPKinesin-like protein KIF11 / 0.654
4qos ADPPsp operon transcriptional activator / 0.653
1xts GTPGTP-binding protein Rheb / 0.651
2ad5 ADPCTP synthase / 0.651
5fv0 ONAESX secretion system protein EccC / 0.651
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.650