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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
4e03 ADP Plasmid partitioning protein ParF

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4e03 ADPPlasmid partitioning protein ParF / 0.883
4dzz ADPPlasmid partitioning protein ParF / 0.778
4ihq ADPConserved Archaeal protein / 0.710
2fna ADPUncharacterized protein / 0.703
4gp6 ADPMetallophosphoesterase / 0.703
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.701
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.701
2x2r ADPKinesin-like protein KIF11 / 0.697
4y0v GDPADP-ribosylation factor 1, putative / 0.697
4ylg GDPADP-ribosylation factor 1, putative / 0.697
3rab GNPRas-related protein Rab-3A / 0.696
2fe4 GDPRas-related protein Rab-6B / 0.695
4pjk ADPMyosin-2 heavy chain / 0.695
1jx2 ADPMyosin-2 heavy chain / 0.693
1z2a GDPRas-related protein Rab-23 / 0.693
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.693
4rkf GNPRas-related protein Rab-3 / 0.693
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.692
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.692
2zts ADPUncharacterized protein / 0.692
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.689
4jsy GTPMetallophosphoesterase / 0.689
3oes GNPGTPase RhebL1 / 0.686
2pg2 ADPKinesin-like protein KIF11 / 0.684
4pfp ADPUnconventional myosin-VI / 0.684
4xsg GSPTransforming protein RhoA / 0.684
1wdt GTPElongation factor G (EF-G-2) / 0.683
1xmv ADPProtein RecA / 0.683
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.683
2qen ADPWalker-Type ATPase / 0.683
2uyi ADPKinesin-like protein KIF11 / 0.683
3tlx ADPAdenylate kinase 2 / 0.683
2y65 ADPKinesin heavy chain / 0.680
3thy ADPDNA mismatch repair protein Msh2 / 0.680
4oi2 ADPProtein clpf-1 / 0.679
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.679
3zia ATPATP synthase subunit alpha, mitochondrial / 0.677
4goj GNPADP-ribosylation factor-like protein 3 / 0.677
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.676
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.676
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.675
3pit GNPRas-related protein M-Ras / 0.675
1z0d GDPRas-related protein Rab-5C / 0.674
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.674
3i3s GNPGTPase HRas / 0.674
3k8y GNPGTPase HRas / 0.674
3kko GNPRas-related protein M-Ras / 0.674
3x1z GNPRas-related protein Rap-1b / 0.674
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.673
4l8g GDPGTPase KRas / 0.673
4wa7 GDPGTPase KRas / 0.673
1p9w ANPType II secretion system protein E / 0.672
2bbw GP5Adenylate kinase 4, mitochondrial / 0.672
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.672
3kkq GDPRas-related protein M-Ras / 0.672
4luc GDPGTPase KRas / 0.672
4obe GDPGTPase KRas / 0.672
4epw GDPGTPase KRas / 0.671
5k5z ANPUncharacterized protein / 0.671
4l9s GDPGTPase HRas / 0.670
1nly AGSCag alpha / 0.669
2hld ANPATP synthase subunit alpha, mitochondrial / 0.669
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.669
4lv6 GDPGTPase KRas / 0.669
4pjj ADPUnconventional myosin-VI / 0.669
4ql3 GDPGTPase KRas / 0.669
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.668
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.668
3x1w GDPRas-related protein Rap-1b / 0.668
4hdq GNPRas-related protein Rap-1b / 0.668
4ldj GDPGTPase KRas / 0.668
4q03 GDPGTPase KRas / 0.668
1ow3 GDPTransforming protein RhoA / 0.667
3r9i ADPSeptum site-determining protein MinD / 0.667
5bn3 ADPV-type ATP synthase alpha chain / 0.667
5bn3 ADPNEQ263 / 0.667
5ftc ADPTPR domain protein / 0.667
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.666
1f5n GNPGuanylate-binding protein 1 / 0.665
1d5c GDPGTPase (Rab6) / 0.664
2q3f GNPRas-related GTP-binding protein D / 0.664
1rj9 GCPSignal recognition particle receptor FtsY / 0.663
1z6t ADPApoptotic protease-activating factor 1 / 0.663
3tqc ADPPantothenate kinase / 0.663
1s1c GNPTransforming protein RhoA / 0.662
2vf7 ADPUvrABC system protein A / 0.662
4jjz ADPFormate--tetrahydrofolate ligase / 0.661
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.661
3jvv ACPTwitching mobility protein / 0.660
4epx GDPGTPase KRas / 0.660
2zet GTPRas-related protein Rab-27B / 0.659
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.659
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.659
1a2b GSPTransforming protein RhoA / 0.658
4jl6 ADPAdenylate kinase / 0.658
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.657
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.657
1oix GDPRas-related protein Rab-11A / 0.657
2dpx GDPGTP-binding protein RAD / 0.657
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.657
4ncl GDPEukaryotic translation initiation factor 5B / 0.657
4ohx ADPProtein clpf-1 / 0.657
2dft ADPShikimate kinase 2.7.1.71 0.656
4jl5 ADPAdenylate kinase / 0.656
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.655
1sdm ADPKinesin heavy chain-like protein / 0.655
3cob ADPKinesin heavy chain-like protein / 0.655
4uj5 GNPRas-related protein Rab-11A / 0.655
1ank ANPAdenylate kinase / 0.654
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.654
4a28 ADPKinesin-like protein KIF11 / 0.654
4tq9 GDPGTPase KRas / 0.654
1w5s ADPORC1-type DNA replication protein 2 / 0.653
1yrs ADPKinesin-like protein KIF11 / 0.653
1z0f GDPRas-related protein Rab-14 / 0.653
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.653
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.653
2x7e ADPKinesin-like protein KIF11 / 0.652
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.651
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.651
4jlo ADPAdenylate kinase / 0.651
1sq5 ADPPantothenate kinase 2.7.1.33 0.650
1x1r GDPRas-related protein M-Ras / 0.650
1xms ANPProtein RecA / 0.650
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650