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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
2d4h 5GP Guanylate-binding protein 1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2d4h 5GPGuanylate-binding protein 1 / 1.001
2y65 ADPKinesin heavy chain / 0.710
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.695
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.693
1wbb ADPDNA mismatch repair protein MutS / 0.691
1cxz GSPTransforming protein RhoA / 0.687
1gwn GTPRho-related GTP-binding protein RhoE / 0.687
2fl2 ADPKinesin-like protein KIF11 / 0.686
1xmv ADPProtein RecA / 0.684
1ow3 GDPTransforming protein RhoA / 0.683
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.682
1svl ADPLarge T antigen 3.6.4 0.681
3kkq GDPRas-related protein M-Ras / 0.680
4lpk GDPGTPase KRas / 0.680
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.680
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.679
2ffq GSPRas-related protein Rab-6B / 0.677
2xae ADPKinesin-like protein KIF11 / 0.677
3cf0 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.677
4luc GDPGTPase KRas / 0.676
4xvq GNPGTPase HRas / 0.673
2r9v ATPATP synthase subunit alpha / 0.672
3mjh GTPRas-related protein Rab-5A / 0.672
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.671
2uyi ADPKinesin-like protein KIF11 / 0.669
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.669
4qbh AP5Adenylate kinase / 0.669
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.668
4obe GDPGTPase KRas / 0.668
1jx2 ADPMyosin-2 heavy chain / 0.667
1ny5 ADPTranscriptional regulator (NtrC family) / 0.667
2c9c ATPPsp operon transcriptional activator / 0.667
2zfi ADPKinesin-like protein KIF1A / 0.667
3qi2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.667
2dr3 ADPUPF0273 protein PH0284 / 0.666
4l8g GDPGTPase KRas / 0.665
4l9s GDPGTPase HRas / 0.664
4ldj GDPGTPase KRas / 0.664
1a2b GSPTransforming protein RhoA / 0.663
1fnn ADPORC1-type DNA replication protein / 0.663
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.663
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.663
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.663
4epw GDPGTPase KRas / 0.663
4qos ADPPsp operon transcriptional activator / 0.663
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.663
4epx GDPGTPase KRas / 0.662
4pfp ADPUnconventional myosin-VI / 0.662
4q02 GDPGTPase KRas / 0.662
4q03 GDPGTPase KRas / 0.662
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.662
2pg2 ADPKinesin-like protein KIF11 / 0.661
2qen ADPWalker-Type ATPase / 0.661
3l9h ADPKinesin-like protein KIF11 / 0.661
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.661
2ql6 ADPNicotinamide riboside kinase 1 / 0.660
3x1w GDPRas-related protein Rap-1b / 0.659
4lrw GDPGTPase KRas / 0.659
1b7t ADPMyosin heavy chain, striated muscle / 0.657
2bc9 GNPGuanylate-binding protein 1 / 0.656
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.656
4z54 GDPNeuronal-specific septin-3 / 0.654
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
1yrs ADPKinesin-like protein KIF11 / 0.653
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.652
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.652
2dpx GDPGTP-binding protein RAD / 0.652
4g01 GDPRas-related protein RABF2b / 0.652
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.652
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.651
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.650