Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
1svw GTP Probable GTP-binding protein EngB

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1svw GTPProbable GTP-binding protein EngB / 1.084
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.824
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.814
1ibr GNPGTP-binding nuclear protein Ran / 0.801
3b1x GNPFerrous iron transport protein B / 0.793
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.790
3vhx GTPADP-ribosylation factor 6 / 0.789
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.788
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.784
1t91 GTPRas-related protein Rab-7a / 0.783
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.783
3tjz GNPADP-ribosylation factor 1 / 0.783
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.779
4xoi GTPTransforming protein RhoA / 0.778
4rkf GNPRas-related protein Rab-3 / 0.774
2j5x GSPADP-ribosylation factor 6 / 0.771
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.767
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.766
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.763
3oiu GNPGTPase HRas / 0.763
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.762
5dif GNPGTP-binding nuclear protein Ran / 0.762
3x1z GNPRas-related protein Rap-1b / 0.760
4tq9 GDPGTPase KRas / 0.760
2c5l GTPGTPase HRas / 0.758
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.758
4goj GNPADP-ribosylation factor-like protein 3 / 0.757
4hdo GNPRas-related protein Rap-1b / 0.757
4js0 GNPCell division control protein 42 homolog / 0.755
3kkq GDPRas-related protein M-Ras / 0.753
3tkl GTPRas-related protein Rab-1A / 0.753
3wyf GTPGTP-binding nuclear protein / 0.752
5b2z GNPGTPase HRas / 0.751
1z2a GDPRas-related protein Rab-23 / 0.750
2ffq GSPRas-related protein Rab-6B / 0.750
3kz1 GSPTransforming protein RhoA / 0.750
4dls GNPGTPase HRas / 0.750
4dvg GSPRho family GTPase / 0.750
4l9w GNPGTPase HRas / 0.750
2cls GTPRho-related GTP-binding protein Rho6 / 0.749
2fg5 GNPRas-related protein Rab-31 / 0.749
4lhw GNPRas-related protein Rab-8A / 0.749
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.747
4hdq GNPRas-related protein Rap-1b / 0.747
2rgb GNPGTPase HRas / 0.746
2xtn GTPGTPase IMAP family member 2 / 0.746
3bbp GTPRas-related protein Rab-6A / 0.746
3v4f GNPGTPase HRas / 0.746
4dlz GNPGTPase HRas / 0.745
1g16 GDPRas-related protein SEC4 / 0.744
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.744
3tso GNPRas-related protein Rab-25 / 0.744
4dsn GCPGTPase KRas / 0.744
2bme GNPRas-related protein Rab-4A / 0.743
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.743
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.743
4kvg GTPRas-related protein Rap-1A / 0.743
3r9x GNPGTPase Era / 0.742
1wa5 GTPGTP-binding nuclear protein Ran / 0.741
4dso GSPGTPase KRas / 0.741
4lrw GDPGTPase KRas / 0.741
3eg5 GNPCell division control protein 42 homolog / 0.740
4ncl GDPEukaryotic translation initiation factor 5B / 0.740
1gwn GTPRho-related GTP-binding protein RhoE / 0.739
1z0d GDPRas-related protein Rab-5C / 0.739
3w3z GTPGTP-binding nuclear protein Ran / 0.739
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.739
2rgg GNPGTPase HRas / 0.738
1a2b GSPTransforming protein RhoA / 0.737
4y0v GDPADP-ribosylation factor 1, putative / 0.737
4ylg GDPADP-ribosylation factor 1, putative / 0.737
1kmq GNPTransforming protein RhoA / 0.736
1lfd GNPGTPase HRas / 0.736
4l9s GDPGTPase HRas / 0.735
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.735
3ddc GNPGTPase HRas / 0.734
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.734
4wa7 GDPGTPase KRas / 0.734
4o2l GTPGTP-binding protein Rheb / 0.733
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.733
4qxa GTPRas-related protein Rab-9A / 0.733
2gcp GSPRho-related GTP-binding protein RhoC / 0.732
3mjh GTPRas-related protein Rab-5A / 0.732
5di3 GNPADP-ribosylation factor-like protein 3 / 0.732
2gil GTPRas-related protein Rab-6A / 0.731
3kko GNPRas-related protein M-Ras / 0.731
3ref GDPRho family GTPase / 0.731
3tgp GNPGTPase HRas / 0.731
3l8y GNPGTPase HRas / 0.730
4dlt GNPGTPase HRas / 0.730
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.728
1fmw ATPMyosin-2 heavy chain / 0.727
1uad GNPRas-related protein Ral-A / 0.725
1zc4 GNPRas-related protein Ral-A / 0.725
3lbh GNPGTPase HRas / 0.725
3rs7 GNPGTPase HRas / 0.725
4lv6 GDPGTPase KRas / 0.725
3ieu GDPGTPase Era / 0.724
1g17 GNPRas-related protein SEC4 / 0.723
3t1t GDPProbable gliding protein mglA / 0.723
2bku GTPGTP-binding nuclear protein Ran / 0.722
4qm6 GTPMetallophosphoesterase / 0.722
4xsg GSPTransforming protein RhoA / 0.722
3kuc GDPRas-related protein Rap-1A / 0.721
4itr GDPCell division control protein 42 homolog / 0.721
2cl6 CAGGTPase HRas / 0.720
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.720
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.720
3rs4 GNPGTPase HRas / 0.720
3x1w GDPRas-related protein Rap-1b / 0.720
4dlx GNPGTPase HRas / 0.720
3lbn GNPGTPase HRas / 0.719
4k81 GTPGTPase HRas / 0.719
4ldj GDPGTPase KRas / 0.719
4ol0 GTPGTP-binding nuclear protein Ran / 0.719
1z0a GDPRas-related protein Rab-2A / 0.718
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.718
4dsu GDPGTPase KRas / 0.718
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.717
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.716
3k8y GNPGTPase HRas / 0.716
3qbt GNPRas-related protein Rab-8A / 0.716
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.716
4epx GDPGTPase KRas / 0.716
4q02 GDPGTPase KRas / 0.716
3rs0 GNPGTPase HRas / 0.715
3rs5 GNPGTPase HRas / 0.715
3rsl GNPGTPase HRas / 0.715
1m7b GTPRho-related GTP-binding protein RhoE / 0.714
1yra GDPGPN-loop GTPase PAB0955 / 0.714
1yu9 GNPRas-related protein Rab-4A / 0.714
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.713
3ea5 GDPGTP-binding nuclear protein Ran / 0.713
3pit GNPRas-related protein M-Ras / 0.713
4d0l GSPRas-related protein Rab-11A / 0.713
4dlw GNPGTPase HRas / 0.713
4o25 GTPGTP-binding protein Rheb / 0.713
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.712
1tu3 GNPRas-related protein Rab-5A / 0.712
5l3s GNPSignal recognition particle receptor FtsY / 0.712
1mmg AGSMyosin-2 heavy chain / 0.710
1xts GTPGTP-binding protein Rheb / 0.710
2q3f GNPRas-related GTP-binding protein D / 0.710
4xvq GNPGTPase HRas / 0.710
1yzq GNPRas-related protein Rab-6A / 0.709
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.708
1x1r GDPRas-related protein M-Ras / 0.707
2fe4 GDPRas-related protein Rab-6B / 0.707
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.706
3nbz GTPGTP-binding nuclear protein Ran / 0.706
4mkf AP5Adenylate kinase / 0.706
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.705
2rgc GNPGTPase HRas / 0.704
3a58 GNPGTP-binding protein RHO1 / 0.704
3oiw GNPGTPase HRas / 0.704
4q03 GDPGTPase KRas / 0.704
3oiv GNPGTPase HRas / 0.703
4ql3 GDPGTPase KRas / 0.703
3dl0 AP5Adenylate kinase / 0.702
5c46 GSPRas-related protein Rab-11A / 0.701
2rge GNPGTPase HRas / 0.700
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.699
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.699
5dha GNPGTP-binding nuclear protein Ran / 0.699
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.698
3bc1 GNPRas-related protein Rab-27A / 0.698
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.698
4mit GTPRho-related protein racC / 0.698
3dkv AP5Adenylate kinase / 0.697
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.695
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.695
2j7p GNPSignal recognition particle protein / 0.693
2j7p GNPSignal recognition particle receptor FtsY / 0.693
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.693
1esn ANPPantothenate kinase 2.7.1.33 0.692
1vg8 GNPRas-related protein Rab-7a / 0.692
3a6p GTPGTP-binding nuclear protein Ran / 0.692
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.692
3m0e ATPTranscriptional regulator (NtrC family) / 0.692
4luc GDPGTPase KRas / 0.692
4g01 GDPRas-related protein RABF2b / 0.691
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.690
1zc3 GNPRas-related protein Ral-A / 0.690
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.690
3lbi GNPGTPase HRas / 0.690
4jsy GTPMetallophosphoesterase / 0.690
1okk GCPSignal recognition particle protein / 0.689
1okk GCPSignal recognition particle receptor FtsY / 0.689
1z2c GNPRho-related GTP-binding protein RhoC / 0.689
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.689
3oes GNPGTPase RhebL1 / 0.689
5jlj GNPGTP-binding nuclear protein Ran / 0.689
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.688
4epw GDPGTPase KRas / 0.687
4mkg AP5Adenylate kinase / 0.686
1rj9 GCPSignal recognition particle receptor FtsY / 0.685
1z0f GDPRas-related protein Rab-14 / 0.685
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.685
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.685
3k9l GNPGTPase HRas / 0.685
4w5j AP5Adenylate kinase / 0.685
1p3j AP5Adenylate kinase / 0.684
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.684
4dlv GNPGTPase HRas / 0.684
2c96 ATPPsp operon transcriptional activator / 0.683
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.683
4lhv GDPRas-related protein Rab-8A / 0.683
1mma ADPMyosin-2 heavy chain / 0.682
1zbd GTPRas-related protein Rab-3A / 0.682
2osb AP5Adenylate kinase / 0.682
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.682
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.682
2fl2 ADPKinesin-like protein KIF11 / 0.681
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.680
2eu8 AP5Adenylate kinase / 0.680
4l8g GDPGTPase KRas / 0.680
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.679
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
1f5n GNPGuanylate-binding protein 1 / 0.679
2oo7 AP5Adenylate kinase / 0.679
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.679
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.679
1k5d GNPGTP-binding nuclear protein Ran / 0.678
2dpx GDPGTP-binding protein RAD / 0.678
5aun ADPIron-sulfur cluster carrier protein / 0.678
1jx2 ADPMyosin-2 heavy chain / 0.677
1z6t ADPApoptotic protease-activating factor 1 / 0.676
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.676
4ike ADPAdenylate kinase / 0.675
2ad5 ADPCTP synthase / 0.674
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.673
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
4nu0 AP5Adenylate kinase / 0.672
1l8q ADPChromosomal replication initiator protein DnaA / 0.671
4qbg AP5Adenylate kinase / 0.671
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.670
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.670
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.670
2xto GDPGTPase IMAP family member 2 / 0.669
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.669
3i3s GNPGTPase HRas / 0.669
4b7b ADPKinesin-like protein KIF11 / 0.669
1cxz GSPTransforming protein RhoA / 0.668
2aky AP5Adenylate kinase / 0.668
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.668
4g0n GNPGTPase HRas / 0.668
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.667
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
1loo GTPAdenylosuccinate synthetase isozyme 1 / 0.667
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.667
3law GNPRas-related protein Rab-7a / 0.666
4a1z ADPKinesin-like protein KIF11 / 0.666
4uj5 GNPRas-related protein Rab-11A / 0.666
1tg5 6454-hydroxyphenylpyruvate dioxygenase 1.13.11.27 0.665
2r9v ATPATP synthase subunit alpha / 0.665
5da9 AGSUncharacterized protein / 0.665
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.664
3fgo CZASarcoplasmic/endoplasmic reticulum calcium ATPase 1 3.6.3.8 0.664
3tqc ADPPantothenate kinase / 0.664
1t47 NTD4-hydroxyphenylpyruvate dioxygenase 1.13.11.27 0.663
3pcr GTPADP-ribosylation factor 6 / 0.663
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.663
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.662
4hse ADPChaperone protein ClpB / 0.662
4xvu ATPATPase GET3 / 0.662
1ny5 ADPTranscriptional regulator (NtrC family) / 0.661
1pl6 572Sorbitol dehydrogenase 1.1.1.14 0.661
1tfz 8694-hydroxyphenylpyruvate dioxygenase 1.13.11.27 0.661
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.661
2zet GTPRas-related protein Rab-27B / 0.661
2zrf DTPProtein RecA / 0.661
3pcn DHYProtocatechuate 3,4-dioxygenase alpha chain 1.13.11.3 0.661
3pcn DHYProtocatechuate 3,4-dioxygenase beta chain 1.13.11.3 0.661
4c2u ANPDNA helicase / 0.661
4v02 ATPSite-determining protein / 0.661
1n6l GTPRas-related protein Rab-5A / 0.660
1sa4 JANProtein farnesyltransferase subunit beta 2.5.1.58 0.660
2iej S48Protein farnesyltransferase subunit beta 2.5.1.58 0.660
3k14 5352-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 0.660
3o3j BB4Peptide deformylase 1B, chloroplastic/mitochondrial 3.5.1.88 0.660
3pz3 PZ3Geranylgeranyl transferase type-2 subunit beta 2.5.1.60 0.660
3pz4 3PZProtein farnesyltransferase subunit beta 2.5.1.58 0.660
3sfx JANUncharacterized protein / 0.660
3znr NU9Histone deacetylase 7 3.5.1.98 0.660
4gtp 7TPProtein farnesyltransferase subunit beta 2.5.1.58 0.660
4lnb ED5CaaX farnesyltransferase beta subunit Ram1 / 0.660
4lng JANCaaX farnesyltransferase beta subunit Ram1 / 0.660
4nyj GNPGTPase HRas / 0.660
5cto NTD4-hydroxyphenylpyruvate dioxygenase 1.13.11.27 0.660
5kcp PFBAlcohol dehydrogenase E chain 1.1.1.1 0.660
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.658
1b7t ADPMyosin heavy chain, striated muscle / 0.657
1uof PNNDeacetoxycephalosporin C synthase 1.14.20.1 0.657
4pk4 ADPUnconventional myosin-VI / 0.657
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.657
2r6g ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.656
2y6d TQJMatrilysin 3.4.24.23 0.656
4pjk ADPMyosin-2 heavy chain / 0.656
3k1j ADPATP-dependent protease Lon / 0.655
1n2g APCPantothenate synthetase 6.3.2.1 0.654
3kmw ATPIntegrin-linked protein kinase 2.7.11.1 0.654
1fnn ADPORC1-type DNA replication protein / 0.653
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.652
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.652
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.652
1zio AP5Adenylate kinase / 0.651
4i1v ADPDephospho-CoA kinase / 0.651
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.651
2x2r ADPKinesin-like protein KIF11 / 0.650
4ohx ADPProtein clpf-1 / 0.650
5dac AGSUncharacterized protein / 0.650