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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
1nsf ATP Vesicle-fusing ATPase 3.6.4.6

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1nsf ATPVesicle-fusing ATPase 3.6.4.6 1.273
1esn ANPPantothenate kinase 2.7.1.33 0.802
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.796
2j7p GNPSignal recognition particle protein / 0.794
2j7p GNPSignal recognition particle receptor FtsY / 0.794
3q9l ATPSeptum site-determining protein MinD / 0.776
2q3f GNPRas-related GTP-binding protein D / 0.771
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.771
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.758
2fg5 GNPRas-related protein Rab-31 / 0.755
1rj9 GCPSignal recognition particle receptor FtsY / 0.751
4xvu ATPATPase GET3 / 0.748
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.747
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.747
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.739
2cls GTPRho-related GTP-binding protein Rho6 / 0.735
1okk GCPSignal recognition particle protein / 0.733
1okk GCPSignal recognition particle receptor FtsY / 0.733
3ea5 GDPGTP-binding nuclear protein Ran / 0.732
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.725
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.723
4v02 ATPSite-determining protein / 0.722
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.721
3k9l GNPGTPase HRas / 0.720
1yu9 GNPRas-related protein Rab-4A / 0.719
3mjh GTPRas-related protein Rab-5A / 0.719
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.718
3fkq ATPNtrC-like two-domain protein / 0.718
3hqd ANPKinesin-like protein KIF11 / 0.718
3qbt GNPRas-related protein Rab-8A / 0.718
4xoi GTPTransforming protein RhoA / 0.718
3ftq GNPSeptin-2 / 0.717
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.717
2gm1 ADPKinesin-like protein KIF11 / 0.716
3oee ANPATP synthase subunit alpha, mitochondrial / 0.715
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.715
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.714
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.714
3cph GDPRas-related protein SEC4 / 0.714
5dha GNPGTP-binding nuclear protein Ran / 0.714
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.713
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.712
4mit GTPRho-related protein racC / 0.709
1z0d GDPRas-related protein Rab-5C / 0.707
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.706
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.706
2cl6 CAGGTPase HRas / 0.706
1gwn GTPRho-related GTP-binding protein RhoE / 0.705
1wa5 GTPGTP-binding nuclear protein Ran / 0.705
5k5z ANPUncharacterized protein / 0.705
1fmw ATPMyosin-2 heavy chain / 0.704
1k5d GNPGTP-binding nuclear protein Ran / 0.704
4xvr GNPGTPase HRas / 0.703
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.702
3e5h GNPRas-related protein Rab-28 / 0.702
4g0n GNPGTPase HRas / 0.701
1cxz GSPTransforming protein RhoA / 0.700
4hut ATPCob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 0.699
1t91 GTPRas-related protein Rab-7a / 0.698
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.698
2xtn GTPGTPase IMAP family member 2 / 0.697
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.695
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.694
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.693
4lpk GDPGTPase KRas / 0.693
5jlj GNPGTP-binding nuclear protein Ran / 0.693
4xsg GSPTransforming protein RhoA / 0.692
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.691
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.691
2fe4 GDPRas-related protein Rab-6B / 0.691
1xtr GNPGTP-binding protein Rheb / 0.690
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.690
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.690
1z2c GNPRho-related GTP-binding protein RhoC / 0.689
3c41 ANPAmino acid ABC transporter / 0.689
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.689
4q02 GDPGTPase KRas / 0.688
4q03 GDPGTPase KRas / 0.688
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.686
2hld ANPATP synthase subunit alpha, mitochondrial / 0.686
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.686
4lrw GDPGTPase KRas / 0.686
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.685
2whx ADPGenome polyprotein 3.4.21.91 0.684
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.683
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.683
2bme GNPRas-related protein Rab-4A / 0.683
1jx2 ADPMyosin-2 heavy chain / 0.682
3b1x GNPFerrous iron transport protein B / 0.682
4d0l GSPRas-related protein Rab-11A / 0.682
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.682
1n6l GTPRas-related protein Rab-5A / 0.681
4xvq GNPGTPase HRas / 0.681
2r9v ATPATP synthase subunit alpha / 0.680
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.680
4g01 GDPRas-related protein RABF2b / 0.680
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.679
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.679
3zia ATPATP synthase subunit alpha, mitochondrial / 0.679
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.678
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.678
1mmg AGSMyosin-2 heavy chain / 0.678
1v8k ANPKinesin-like protein KIF2C / 0.678
3bc1 GNPRas-related protein Rab-27A / 0.677
1ank ANPAdenylate kinase / 0.676
2bc9 GNPGuanylate-binding protein 1 / 0.676
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.675
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.675
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.675
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.675
3tkl GTPRas-related protein Rab-1A / 0.675
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.674
4dsn GCPGTPase KRas / 0.674
1w5t ANPORC1-type DNA replication protein 2 / 0.673
2c5l GTPGTPase HRas / 0.673
3q5d GDPAtlastin-1 3.6.5 0.673
4dvg GSPRho family GTPase / 0.673
1wbb ADPDNA mismatch repair protein MutS / 0.672
1z2a GDPRas-related protein Rab-23 / 0.672
3myk ANPMyosin-2 heavy chain / 0.672
1am4 GNPCell division control protein 42 homolog / 0.671
1tu3 GNPRas-related protein Rab-5A / 0.671
2qen ADPWalker-Type ATPase / 0.671
3a58 GNPGTP-binding protein RHO1 / 0.671
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.671
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.670
1vg8 GNPRas-related protein Rab-7a / 0.670
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.670
4kvg GTPRas-related protein Rap-1A / 0.670
4ol0 GTPGTP-binding nuclear protein Ran / 0.670
5l3s GNPSignal recognition particle receptor FtsY / 0.670
4pk4 ADPUnconventional myosin-VI / 0.669
1e0j ANPDNA primase/helicase 2.7.7 0.667
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.667
1zc4 GNPRas-related protein Ral-A / 0.667
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.667
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
3m0e ATPTranscriptional regulator (NtrC family) / 0.667
1lfd GNPGTPase HRas / 0.666
1oyy AGSATP-dependent DNA helicase RecQ 3.6.4.12 0.666
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.664
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.664
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.664
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.663
3kko GNPRas-related protein M-Ras / 0.663
4dso GSPGTPase KRas / 0.663
4hyv PEPPyruvate kinase 1 2.7.1.40 0.663
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.663
1rrg GDPADP-ribosylation factor 1 / 0.662
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.661
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
4asu ADPATP synthase subunit alpha, mitochondrial / 0.661
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.661
5ftc ADPTPR domain protein / 0.661
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.660
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
1yra GDPGPN-loop GTPase PAB0955 / 0.660
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.660
4dxa GSPRas-related protein Rap-1b / 0.660
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.659
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.659
3lbn GNPGTPase HRas / 0.658
3tso GNPRas-related protein Rab-25 / 0.658
4dsu GDPGTPase KRas / 0.658
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.657
3l8y GNPGTPase HRas / 0.657
3rsl GNPGTPase HRas / 0.657
4ncl GDPEukaryotic translation initiation factor 5B / 0.657
4y0v GDPADP-ribosylation factor 1, putative / 0.657
4ylg GDPADP-ribosylation factor 1, putative / 0.657
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.656
3v4f GNPGTPase HRas / 0.656
4jjz ADPFormate--tetrahydrofolate ligase / 0.656
4l9w GNPGTPase HRas / 0.656
4oi2 ADPProtein clpf-1 / 0.656
4db1 ANPMyosin-7 / 0.655
1sdm ADPKinesin heavy chain-like protein / 0.654
1x1r GDPRas-related protein M-Ras / 0.654
1zbd GTPRas-related protein Rab-3A / 0.654
2bku GTPGTP-binding nuclear protein Ran / 0.654
2rgc GNPGTPase HRas / 0.654
3oiv GNPGTPase HRas / 0.654
3x1w GDPRas-related protein Rap-1b / 0.654
4uj5 GNPRas-related protein Rab-11A / 0.654
3vhx GTPADP-ribosylation factor 6 / 0.653
3wyf GTPGTP-binding nuclear protein / 0.653
4hse ADPChaperone protein ClpB / 0.653
4ohw ATPProtein clpf-1 / 0.653
4yqf GDPSeptin-9 / 0.653
1xms ANPProtein RecA / 0.652
3rs0 GNPGTPase HRas / 0.652
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.651
4js0 GNPCell division control protein 42 homolog / 0.651
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.651
2c9c ATPPsp operon transcriptional activator / 0.650
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.650
3oes GNPGTPase RhebL1 / 0.650
3rs4 GNPGTPase HRas / 0.650
4dlv GNPGTPase HRas / 0.650
5di3 GNPADP-ribosylation factor-like protein 3 / 0.650