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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
3sop GDP Neuronal-specific septin-3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3sop GDPNeuronal-specific septin-3 / 0.934
1eyn 2ANUDP-N-acetylglucosamine 1-carboxyvinyltransferase / 0.744
1sa4 JANProtein farnesyltransferase subunit beta 2.5.1.58 0.744
2f0y 3MNProtein farnesyltransferase subunit beta 2.5.1.58 0.744
2xvv 9DNSerum albumin / 0.744
3cz0 9ODPheromone-binding protein ASP1 / 0.744
3fo7 IMNPhospholipase A2 VRV-PL-VIIIa / 0.744
3k14 5352-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 0.744
3nks ACJProtoporphyrinogen oxidase 1.3.3.4 0.744
3pz4 3PZProtein farnesyltransferase subunit beta 2.5.1.58 0.744
3sfx JANUncharacterized protein / 0.744
3znr NU9Histone deacetylase 7 3.5.1.98 0.744
3zns NU7Histone deacetylase 7 3.5.1.98 0.744
4c1f X8ZMetallo-beta-lactamase type 2 / 0.744
4dsb A8SAbscisic acid receptor PYL3 / 0.744
4ivo ACJProtoporphyrinogen oxidase 1.3.3.4 0.744
4kla CHDFerrochelatase, mitochondrial 4.99.1.1 0.744
4lng JANCaaX farnesyltransferase beta subunit Ram1 / 0.744
5dby DIFSerum albumin / 0.744
5dby NPSSerum albumin / 0.744
5jqb IBPEnvelope glycoprotein / 0.744
5kcp PFBAlcohol dehydrogenase E chain 1.1.1.1 0.744
4yqf GDPSeptin-9 / 0.742
1oix GDPRas-related protein Rab-11A / 0.731
3ftq GNPSeptin-2 / 0.728
4z54 GDPNeuronal-specific septin-3 / 0.723
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.705
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.705
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.702
4dsu GDPGTPase KRas / 0.701
4l9s GDPGTPase HRas / 0.701
3x1w GDPRas-related protein Rap-1b / 0.700
4ldj GDPGTPase KRas / 0.700
4q03 GDPGTPase KRas / 0.700
3kuc GDPRas-related protein Rap-1A / 0.699
4lpk GDPGTPase KRas / 0.699
4lv6 GDPGTPase KRas / 0.699
4ql3 GDPGTPase KRas / 0.698
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.694
2l0x GDPGTP-binding protein Rheb / 0.692
1z0d GDPRas-related protein Rab-5C / 0.686
2ce2 GDPGTPase HRas / 0.686
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.686
4g0n GNPGTPase HRas / 0.686
4q02 GDPGTPase KRas / 0.686
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.685
5cyp GSPSeptin-9 / 0.685
1x1r GDPRas-related protein M-Ras / 0.684
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.683
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.683
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.683
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.682
4cym GCPRas-related protein Rab-32 / 0.682
4epw GDPGTPase KRas / 0.682
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.682
2fna ADPUncharacterized protein / 0.681
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.681
4wa7 GDPGTPase KRas / 0.681
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.680
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.680
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.680
4epx GDPGTPase KRas / 0.680
1cxz GSPTransforming protein RhoA / 0.679
4itr GDPCell division control protein 42 homolog / 0.679
4l8g GDPGTPase KRas / 0.679
1yrs ADPKinesin-like protein KIF11 / 0.678
1z0f GDPRas-related protein Rab-14 / 0.678
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.678
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.678
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.677
1w5t ANPORC1-type DNA replication protein 2 / 0.677
1wdt GTPElongation factor G (EF-G-2) / 0.676
4lrw GDPGTPase KRas / 0.676
4pk4 ADPUnconventional myosin-VI / 0.676
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.675
4zca ADPKinesin-like protein KIF11 / 0.675
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.674
2x7e ADPKinesin-like protein KIF11 / 0.674
4dso GSPGTPase KRas / 0.674
4nyj GNPGTPase HRas / 0.674
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.674
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.673
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.673
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.673
4o2l GTPGTP-binding protein Rheb / 0.673
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.672
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.672
3wyf GTPGTP-binding nuclear protein / 0.672
1kmq GNPTransforming protein RhoA / 0.671
3kkq GDPRas-related protein M-Ras / 0.671
1sdm ADPKinesin heavy chain-like protein / 0.670
1tu3 GNPRas-related protein Rab-5A / 0.670
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.669
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.669
2y65 ADPKinesin heavy chain / 0.669
3ddc GNPGTPase HRas / 0.669
2cl6 CAGGTPase HRas / 0.668
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.668
1ii6 ADPKinesin-like protein KIF11 / 0.667
1ny5 ADPTranscriptional regulator (NtrC family) / 0.667
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.667
3x1z GNPRas-related protein Rap-1b / 0.667
4asu ADPATP synthase subunit alpha, mitochondrial / 0.667
4tq9 GDPGTPase KRas / 0.667
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.666
3cph GDPRas-related protein SEC4 / 0.666
5cyo GDPSeptin-9 / 0.666
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.665
1xtr GNPGTP-binding protein Rheb / 0.665
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.665
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
3b1x GNPFerrous iron transport protein B / 0.665
3c41 ANPAmino acid ABC transporter / 0.665
3rab GNPRas-related protein Rab-3A / 0.665
4dls GNPGTPase HRas / 0.665
4ncl GDPEukaryotic translation initiation factor 5B / 0.665
4xsg GSPTransforming protein RhoA / 0.665
1l8q ADPChromosomal replication initiator protein DnaA / 0.664
4lhv GDPRas-related protein Rab-8A / 0.664
2dft ADPShikimate kinase 2.7.1.71 0.663
3a58 GNPGTP-binding protein RHO1 / 0.663
4iok ADPFormate--tetrahydrofolate ligase / 0.663
4ww4 ADPRuvB-like helicase / 0.663
2c9o ADPRuvB-like 1 3.6.4.12 0.662
2gil GTPRas-related protein Rab-6A / 0.661
1ake AP5Adenylate kinase / 0.660
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.660
1pl6 572Sorbitol dehydrogenase 1.1.1.14 0.660
1rml NTSFibroblast growth factor 1 / 0.660
1tg5 6454-hydroxyphenylpyruvate dioxygenase 1.13.11.27 0.660
2qd3 CHDFerrochelatase, mitochondrial 4.99.1.1 0.660
3fgo CZASarcoplasmic/endoplasmic reticulum calcium ATPase 1 3.6.3.8 0.660
3oee ANPATP synthase subunit alpha, mitochondrial / 0.660
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
3pcn DHYProtocatechuate 3,4-dioxygenase alpha chain 1.13.11.3 0.660
3pcn DHYProtocatechuate 3,4-dioxygenase beta chain 1.13.11.3 0.660
4pxx CHDCarbonic anhydrase 2 4.2.1.1 0.660
5cto NTD4-hydroxyphenylpyruvate dioxygenase 1.13.11.27 0.660
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
1lfd GNPGTPase HRas / 0.659
1ow3 GDPTransforming protein RhoA / 0.659
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.659
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
3eg5 GNPCell division control protein 42 homolog / 0.658
5aun ADPIron-sulfur cluster carrier protein / 0.658
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.657
5ftc ADPTPR domain protein / 0.657
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.656
1n6l GTPRas-related protein Rab-5A / 0.656
1xms ANPProtein RecA / 0.656
4b7b ADPKinesin-like protein KIF11 / 0.656
4hdq GNPRas-related protein Rap-1b / 0.656
4obe GDPGTPase KRas / 0.656
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
2q2y ADPKinesin-like protein KIF11 / 0.655
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.655
3k1j ADPATP-dependent protease Lon / 0.655
3q5d GDPAtlastin-1 3.6.5 0.655
4o2r GDPGTP-binding protein Rheb / 0.655
1am4 GNPCell division control protein 42 homolog / 0.654
1rrg GDPADP-ribosylation factor 1 / 0.654
2fl2 ADPKinesin-like protein KIF11 / 0.654
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.654
4d0l GSPRas-related protein Rab-11A / 0.654
4jl6 ADPAdenylate kinase / 0.654
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.653
1uad GNPRas-related protein Ral-A / 0.653
1zc3 GNPRas-related protein Ral-A / 0.653
3kud GDPGTPase HRas / 0.653
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.653
4xoi GTPTransforming protein RhoA / 0.653
1svl ADPLarge T antigen 3.6.4 0.652
1yzq GNPRas-related protein Rab-6A / 0.652
3lbh GNPGTPase HRas / 0.652
1a2b GSPTransforming protein RhoA / 0.651
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.651
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
2d7d ADPUvrABC system protein B / 0.651
3cob ADPKinesin heavy chain-like protein / 0.651
3l9h ADPKinesin-like protein KIF11 / 0.651
4hdo GNPRas-related protein Rap-1b / 0.651
4pjj ADPUnconventional myosin-VI / 0.651