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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
1xp8 AGS Protein RecA

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1xp8 AGSProtein RecA / 1.040
2zro ADPProtein RecA / 0.875
1xmv ADPProtein RecA / 0.850
2zrj AGSProtein RecA / 0.822
3wyf GTPGTP-binding nuclear protein / 0.720
3ea5 GDPGTP-binding nuclear protein Ran / 0.719
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.717
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.713
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.713
1sdm ADPKinesin heavy chain-like protein / 0.709
3tkl GTPRas-related protein Rab-1A / 0.708
1svm ATPLarge T antigen 3.6.4 0.706
3pcr GTPADP-ribosylation factor 6 / 0.703
3vhx GTPADP-ribosylation factor 6 / 0.701
1xms ANPProtein RecA / 0.697
4lrw GDPGTPase KRas / 0.696
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.694
4a51 ADPKinesin-like protein KIF11 / 0.694
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.693
3qbv GDPCell division control protein 42 homolog / 0.693
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.692
4dxa GSPRas-related protein Rap-1b / 0.692
2dr3 ADPUPF0273 protein PH0284 / 0.691
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.690
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.690
5dac AGSUncharacterized protein / 0.690
3l9h ADPKinesin-like protein KIF11 / 0.689
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.687
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.687
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.686
3w3z GTPGTP-binding nuclear protein Ran / 0.686
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.685
2x2r ADPKinesin-like protein KIF11 / 0.685
2gil GTPRas-related protein Rab-6A / 0.684
2xae ADPKinesin-like protein KIF11 / 0.684
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.683
3tlx ADPAdenylate kinase 2 / 0.683
2uyi ADPKinesin-like protein KIF11 / 0.682
1b7t ADPMyosin heavy chain, striated muscle / 0.677
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.677
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.676
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.676
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.676
4pjk ADPMyosin-2 heavy chain / 0.676
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.675
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.675
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.674
1rrg GDPADP-ribosylation factor 1 / 0.674
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.674
2bku GTPGTP-binding nuclear protein Ran / 0.672
4o2r GDPGTP-binding protein Rheb / 0.672
4ol0 GTPGTP-binding nuclear protein Ran / 0.671
5cyo GDPSeptin-9 / 0.670
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.669
4a1z ADPKinesin-like protein KIF11 / 0.669
4y0v GDPADP-ribosylation factor 1, putative / 0.669
4ylg GDPADP-ribosylation factor 1, putative / 0.669
2pg2 ADPKinesin-like protein KIF11 / 0.668
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.668
3nbz GTPGTP-binding nuclear protein Ran / 0.666
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.665
1wbb ADPDNA mismatch repair protein MutS / 0.665
4dzz ADPPlasmid partitioning protein ParF / 0.665
4jsy GTPMetallophosphoesterase / 0.665
4cf7 ADPAdenylate kinase / 0.664
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.664
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.663
4nu0 AP5Adenylate kinase / 0.662
4w5j AP5Adenylate kinase / 0.661
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.660
1m7b GTPRho-related GTP-binding protein RhoE / 0.660
2cls GTPRho-related GTP-binding protein Rho6 / 0.660
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
1d5c GDPGTPase (Rab6) / 0.659
2zr9 DTPProtein RecA / 0.659
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.658
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.658
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.657
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.656
3myk ANPMyosin-2 heavy chain / 0.655
4pk4 ADPUnconventional myosin-VI / 0.655
1t91 GTPRas-related protein Rab-7a / 0.652
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.652
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.652
1v8k ANPKinesin-like protein KIF2C / 0.651
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.651
2o8b ADPDNA mismatch repair protein Msh2 / 0.651
2zfi ADPKinesin-like protein KIF1A / 0.651
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.650
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.650
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.650
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
2whx ADPGenome polyprotein 3.4.21.91 0.650
3tqc ADPPantothenate kinase / 0.650
4oi2 ADPProtein clpf-1 / 0.650
4uxj TTPThymidine kinase / 0.650