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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
2vf7 ADP UvrABC system protein A

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2vf7 ADPUvrABC system protein A / 1.002
4asu ADPATP synthase subunit alpha, mitochondrial / 0.759
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.753
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.747
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.747
1z2a GDPRas-related protein Rab-23 / 0.746
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.746
2pg2 ADPKinesin-like protein KIF11 / 0.746
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.746
2uyi ADPKinesin-like protein KIF11 / 0.745
3r9i ADPSeptum site-determining protein MinD / 0.745
3hpr AP5Adenylate kinase / 0.742
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.742
4d81 ADPAAA ATPase, central domain protein / 0.741
4x8l AP5Adenylate kinase / 0.741
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.739
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.735
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.735
1cxz GSPTransforming protein RhoA / 0.733
1z0f GDPRas-related protein Rab-14 / 0.733
4ldj GDPGTPase KRas / 0.733
5aun ADPIron-sulfur cluster carrier protein / 0.733
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.731
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.731
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.731
4q03 GDPGTPase KRas / 0.731
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.729
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.729
1t91 GTPRas-related protein Rab-7a / 0.727
2c5l GTPGTPase HRas / 0.726
3mjh GTPRas-related protein Rab-5A / 0.726
4mkf AP5Adenylate kinase / 0.726
3m0e ATPTranscriptional regulator (NtrC family) / 0.725
4mkh AP5Adenylate kinase / 0.725
4tyq AP5Adenylate kinase / 0.724
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.723
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.723
3zia ATPATP synthase subunit alpha, mitochondrial / 0.721
4x8o AP5Adenylate kinase / 0.721
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.719
4xoi GTPTransforming protein RhoA / 0.719
1a2b GSPTransforming protein RhoA / 0.718
1mab ATPATP synthase subunit alpha, mitochondrial / 0.718
1p3j AP5Adenylate kinase / 0.718
2gil GTPRas-related protein Rab-6A / 0.718
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.717
1zbd GTPRas-related protein Rab-3A / 0.717
3cob ADPKinesin heavy chain-like protein / 0.717
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.716
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.716
5fl3 ADPPili retraction protein PilT / 0.716
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.715
2l0x GDPGTP-binding protein Rheb / 0.715
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.715
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.715
1e4v AP5Adenylate kinase / 0.714
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.714
4gp6 ADPMetallophosphoesterase / 0.714
4qxa GTPRas-related protein Rab-9A / 0.714
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.713
3q9l ATPSeptum site-determining protein MinD / 0.713
4qbg AP5Adenylate kinase / 0.713
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.713
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.712
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.712
4dzz ADPPlasmid partitioning protein ParF / 0.712
1wdt GTPElongation factor G (EF-G-2) / 0.711
4ihq ADPConserved Archaeal protein / 0.711
4ncl GDPEukaryotic translation initiation factor 5B / 0.711
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.708
1wa5 GTPGTP-binding nuclear protein Ran / 0.708
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.706
2c9o ADPRuvB-like 1 3.6.4.12 0.706
5dif GNPGTP-binding nuclear protein Ran / 0.705
3ddc GNPGTPase HRas / 0.704
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.702
3law GNPRas-related protein Rab-7a / 0.702
4xsg GSPTransforming protein RhoA / 0.702
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.701
1yu9 GNPRas-related protein Rab-4A / 0.701
3ftq GNPSeptin-2 / 0.701
3ref GDPRho family GTPase / 0.701
4js0 GNPCell division control protein 42 homolog / 0.701
3l9h ADPKinesin-like protein KIF11 / 0.699
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.698
1x1r GDPRas-related protein M-Ras / 0.698
4idn GNPAtlastin-1 3.6.5 0.698
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.698
1nly AGSCag alpha / 0.697
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.697
4q02 GDPGTPase KRas / 0.697
1yra GDPGPN-loop GTPase PAB0955 / 0.696
4xvq GNPGTPase HRas / 0.696
4qos ADPPsp operon transcriptional activator / 0.695
2bme GNPRas-related protein Rab-4A / 0.694
2zrj AGSProtein RecA / 0.694
2bc9 GNPGuanylate-binding protein 1 / 0.693
1rj9 GCPSignal recognition particle receptor FtsY / 0.692
1oix GDPRas-related protein Rab-11A / 0.691
2rgc GNPGTPase HRas / 0.691
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.691
2zr9 DTPProtein RecA / 0.690
3myk ANPMyosin-2 heavy chain / 0.690
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.690
4v02 ATPSite-determining protein / 0.690
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.689
4luc GDPGTPase KRas / 0.689
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
3kko GNPRas-related protein M-Ras / 0.688
3pit GNPRas-related protein M-Ras / 0.688
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.687
2osb AP5Adenylate kinase / 0.687
3tgp GNPGTPase HRas / 0.687
3pcr GTPADP-ribosylation factor 6 / 0.686
4hdq GNPRas-related protein Rap-1b / 0.684
4xvr GNPGTPase HRas / 0.684
1h6d NDPGlucose--fructose oxidoreductase 1.1.99.28 0.683
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.683
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
1g16 GDPRas-related protein SEC4 / 0.682
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.682
2rgg GNPGTPase HRas / 0.682
3c41 ANPAmino acid ABC transporter / 0.682
4lv6 GDPGTPase KRas / 0.682
1ii6 ADPKinesin-like protein KIF11 / 0.681
1z0d GDPRas-related protein Rab-5C / 0.681
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.681
3e5h GNPRas-related protein Rab-28 / 0.681
4qbh AP5Adenylate kinase / 0.681
4db1 ANPMyosin-7 / 0.680
4iok ADPFormate--tetrahydrofolate ligase / 0.680
4oi2 ADPProtein clpf-1 / 0.680
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.679
4epx GDPGTPase KRas / 0.679
2fna ADPUncharacterized protein / 0.678
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.678
5a06 NDPGlucose-fructose oxidoreductase / 0.678
3nbx ADPATPase RavA 3.6.3 0.677
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.676
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.676
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.676
1evj NADGlucose--fructose oxidoreductase 1.1.99.28 0.675
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.675
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.675
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.675
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.675
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.674
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.674
1zio AP5Adenylate kinase / 0.674
3l8y GNPGTPase HRas / 0.674
4dlv GNPGTPase HRas / 0.674
4dso GSPGTPase KRas / 0.674
2zfi ADPKinesin-like protein KIF1A / 0.673
3ieu GDPGTPase Era / 0.673
3lbi GNPGTPase HRas / 0.673
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.673
1xmv ADPProtein RecA / 0.672
4dlz GNPGTPase HRas / 0.672
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.670
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.670
1fmw ATPMyosin-2 heavy chain / 0.670
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.670
3hpq AP5Adenylate kinase / 0.669
3tnf GNPRas-related protein Rab-8A / 0.669
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.669
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.668
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
3i3s GNPGTPase HRas / 0.668
4jsy GTPMetallophosphoesterase / 0.668
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.668
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.668
1esn ANPPantothenate kinase 2.7.1.33 0.667
3k8y GNPGTPase HRas / 0.667
3oes GNPGTPase RhebL1 / 0.667
4g0n GNPGTPase HRas / 0.667
1z0a GDPRas-related protein Rab-2A / 0.666
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.666
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.665
1zc4 GNPRas-related protein Ral-A / 0.665
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.665
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.664
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
3b1x GNPFerrous iron transport protein B / 0.664
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.663
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.663
3q2k NAIProbable oxidoreductase / 0.662
4e03 ADPPlasmid partitioning protein ParF / 0.662
4idp GNPAtlastin-1 3.6.5 0.662
2fg5 GNPRas-related protein Rab-31 / 0.661
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.661
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.661
2q2y ADPKinesin-like protein KIF11 / 0.659
4l16 ADPFidgetin-like protein 1 3.6.4 0.658
5fv0 ONAESX secretion system protein EccC / 0.658
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.657
2zs9 ADPPantothenate kinase 2.7.1.33 0.657
3uk6 ADPRuvB-like 2 3.6.4.12 0.657
4ohx ADPProtein clpf-1 / 0.657
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.657
2zts ADPUncharacterized protein / 0.655
2zsb ADPPantothenate kinase 2.7.1.33 0.654
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.654
4o3m ADPBloom syndrome protein 3.6.4.12 0.654
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.653
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.652
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.652
1svl ADPLarge T antigen 3.6.4 0.652
2ql6 ADPNicotinamide riboside kinase 1 / 0.651
4qm6 GTPMetallophosphoesterase / 0.651
2vor ACPFolylpolyglutamate synthase / 0.650
3qbv GDPCell division control protein 42 homolog / 0.650