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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
4xvu ATP ATPase GET3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4xvu ATPATPase GET3 / 1.169
4v02 ATPSite-determining protein / 0.901
3q9l ATPSeptum site-determining protein MinD / 0.890
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.851
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.824
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.808
1esn ANPPantothenate kinase 2.7.1.33 0.807
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.802
2c5l GTPGTPase HRas / 0.800
1yu9 GNPRas-related protein Rab-4A / 0.799
3oes GNPGTPase RhebL1 / 0.798
4dlw GNPGTPase HRas / 0.792
4idn GNPAtlastin-1 3.6.5 0.792
4xoi GTPTransforming protein RhoA / 0.792
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.791
3k9l GNPGTPase HRas / 0.791
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.790
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.789
4xvq GNPGTPase HRas / 0.789
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.788
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.787
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.786
5di3 GNPADP-ribosylation factor-like protein 3 / 0.783
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.779
1uad GNPRas-related protein Ral-A / 0.778
2rgg GNPGTPase HRas / 0.778
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.776
4g01 GDPRas-related protein RABF2b / 0.776
3tgp GNPGTPase HRas / 0.775
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.768
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.767
2j7p GNPSignal recognition particle protein / 0.766
2j7p GNPSignal recognition particle receptor FtsY / 0.766
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.766
1okk GCPSignal recognition particle protein / 0.764
1okk GCPSignal recognition particle receptor FtsY / 0.764
3wyf GTPGTP-binding nuclear protein / 0.764
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.764
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.762
5l3s GNPSignal recognition particle receptor FtsY / 0.762
3mjh GTPRas-related protein Rab-5A / 0.761
3qbt GNPRas-related protein Rab-8A / 0.761
1d5c GDPGTPase (Rab6) / 0.760
3bbp GTPRas-related protein Rab-6A / 0.760
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.760
4cid ANPEH domain-containing protein 2 / 0.759
1f5n GNPGuanylate-binding protein 1 / 0.757
2q3f GNPRas-related GTP-binding protein D / 0.757
2bme GNPRas-related protein Rab-4A / 0.756
4nh0 ATPESX secretion system protein EccC / 0.756
4qm6 GTPMetallophosphoesterase / 0.756
1mmg AGSMyosin-2 heavy chain / 0.755
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.755
2bc9 GNPGuanylate-binding protein 1 / 0.753
1z2c GNPRho-related GTP-binding protein RhoC / 0.752
4kvg GTPRas-related protein Rap-1A / 0.752
1yzq GNPRas-related protein Rab-6A / 0.751
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.751
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.750
4cym GCPRas-related protein Rab-32 / 0.749
1nsf ATPVesicle-fusing ATPase 3.6.4.6 0.748
1wdt GTPElongation factor G (EF-G-2) / 0.748
3x1z GNPRas-related protein Rap-1b / 0.748
4qbf AP5Adenylate kinase / 0.747
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.746
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.746
1fmw ATPMyosin-2 heavy chain / 0.745
1gwn GTPRho-related GTP-binding protein RhoE / 0.745
2r9v ATPATP synthase subunit alpha / 0.743
3r9x GNPGTPase Era / 0.742
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.742
4k81 GTPGTPase HRas / 0.742
1b7t ADPMyosin heavy chain, striated muscle / 0.740
1w5t ANPORC1-type DNA replication protein 2 / 0.740
2gil GTPRas-related protein Rab-6A / 0.739
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.738
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.738
1m7b GTPRho-related GTP-binding protein RhoE / 0.736
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.735
1cxz GSPTransforming protein RhoA / 0.734
4jlo ADPAdenylate kinase / 0.734
2fg5 GNPRas-related protein Rab-31 / 0.733
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.733
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.732
4goj GNPADP-ribosylation factor-like protein 3 / 0.732
5jlj GNPGTP-binding nuclear protein Ran / 0.732
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.731
4db1 ANPMyosin-7 / 0.731
2eck ADPAdenylate kinase / 0.730
2ffq GSPRas-related protein Rab-6B / 0.730
3e5h GNPRas-related protein Rab-28 / 0.730
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.730
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.728
2j5x GSPADP-ribosylation factor 6 / 0.728
2rgb GNPGTPase HRas / 0.728
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.728
4e07 ACPPlasmid partitioning protein ParF / 0.728
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.728
5dif GNPGTP-binding nuclear protein Ran / 0.728
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.727
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.726
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.726
5b2z GNPGTPase HRas / 0.726
1k5d GNPGTP-binding nuclear protein Ran / 0.724
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.724
4lhw GNPRas-related protein Rab-8A / 0.724
3pit GNPRas-related protein M-Ras / 0.723
3r9i ADPSeptum site-determining protein MinD / 0.723
3ref GDPRho family GTPase / 0.723
4i1v ADPDephospho-CoA kinase / 0.722
1g17 GNPRas-related protein SEC4 / 0.721
4q03 GDPGTPase KRas / 0.721
2rgc GNPGTPase HRas / 0.720
4nyi GNPGTPase HRas / 0.720
4qxa GTPRas-related protein Rab-9A / 0.720
1ake AP5Adenylate kinase / 0.719
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.719
1kmq GNPTransforming protein RhoA / 0.719
1wa5 GTPGTP-binding nuclear protein Ran / 0.719
4dlx GNPGTPase HRas / 0.719
3a6p GTPGTP-binding nuclear protein Ran / 0.718
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.718
3vhx GTPADP-ribosylation factor 6 / 0.718
4dlz GNPGTPase HRas / 0.718
2a5y ATPCell death protein 4 / 0.717
1rj9 GCPSignal recognition particle receptor FtsY / 0.716
3a58 GNPGTP-binding protein RHO1 / 0.716
4hdo GNPRas-related protein Rap-1b / 0.716
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.715
3kud GDPGTPase HRas / 0.715
3w3z GTPGTP-binding nuclear protein Ran / 0.715
3lbh GNPGTPase HRas / 0.714
1n6l GTPRas-related protein Rab-5A / 0.713
1s1c GNPTransforming protein RhoA / 0.713
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.713
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.713
2cl6 CAGGTPase HRas / 0.712
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.712
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.711
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.711
2xtn GTPGTPase IMAP family member 2 / 0.711
1z0f GDPRas-related protein Rab-14 / 0.710
2l0x GDPGTP-binding protein Rheb / 0.710
4jld ADPAdenylate kinase / 0.710
4xvr GNPGTPase HRas / 0.710
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.709
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.709
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.709
3b1x GNPFerrous iron transport protein B / 0.709
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.708
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.708
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
3t1t GDPProbable gliding protein mglA / 0.708
4dxa GSPRas-related protein Rap-1b / 0.708
5dha GNPGTP-binding nuclear protein Ran / 0.708
1a2b GSPTransforming protein RhoA / 0.707
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.707
4dsn GCPGTPase KRas / 0.707
4nyj GNPGTPase HRas / 0.706
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.704
1zc3 GNPRas-related protein Ral-A / 0.704
4jsy GTPMetallophosphoesterase / 0.704
5c46 GSPRas-related protein Rab-11A / 0.703
1zc4 GNPRas-related protein Ral-A / 0.702
2gcp GSPRho-related GTP-binding protein RhoC / 0.702
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.702
3cob ADPKinesin heavy chain-like protein / 0.702
3q5d GDPAtlastin-1 3.6.5 0.702
1zbd GTPRas-related protein Rab-3A / 0.701
2bku GTPGTP-binding nuclear protein Ran / 0.701
3kkq GDPRas-related protein M-Ras / 0.701
4ffb GTPTubulin alpha-1 chain / 0.701
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.700
4js0 GNPCell division control protein 42 homolog / 0.700
4q02 GDPGTPase KRas / 0.699
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.698
5hpy GDPTransforming protein RhoA / 0.698
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.697
1svm ATPLarge T antigen 3.6.4 0.697
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.697
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.696
3hqd ANPKinesin-like protein KIF11 / 0.696
3law GNPRas-related protein Rab-7a / 0.696
4ol0 GTPGTP-binding nuclear protein Ran / 0.696
1vg8 GNPRas-related protein Rab-7a / 0.695
5k5z ANPUncharacterized protein / 0.695
4dvg GSPRho family GTPase / 0.694
4o25 GTPGTP-binding protein Rheb / 0.694
2ce2 GDPGTPase HRas / 0.693
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.693
4xsg GSPTransforming protein RhoA / 0.693
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.692
4hut ATPCob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 0.692
2x7e ADPKinesin-like protein KIF11 / 0.691
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.691
4itr GDPCell division control protein 42 homolog / 0.691
4lhv GDPRas-related protein Rab-8A / 0.691
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.690
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.690
3tkl GTPRas-related protein Rab-1A / 0.690
3tnf GNPRas-related protein Rab-8A / 0.690
4jl6 ADPAdenylate kinase / 0.690
4dso GSPGTPase KRas / 0.689
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.688
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.688
3ea0 ATPATPase, ParA family / 0.688
3rsl GNPGTPase HRas / 0.687
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.686
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.685
4ohw ATPProtein clpf-1 / 0.685
1sxj AGSReplication factor C subunit 1 / 0.684
2zts ADPUncharacterized protein / 0.684
3a37 ADPATPase GET3 / 0.684
3dkv AP5Adenylate kinase / 0.684
3tlx ADPAdenylate kinase 2 / 0.684
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.683
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.683
4zca ADPKinesin-like protein KIF11 / 0.683
2hld ANPATP synthase subunit alpha, mitochondrial / 0.682
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
3b05 IPEIsopentenyl-diphosphate delta-isomerase / 0.682
3kb1 ADPIron-sulfur cluster carrier protein / 0.682
4jl5 ADPAdenylate kinase / 0.682
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.681
1xtr GNPGTP-binding protein Rheb / 0.681
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.681
3tso GNPRas-related protein Rab-25 / 0.681
4fyx UTPAspartate carbamoyltransferase regulatory chain / 0.681
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.681
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.680
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.680
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.680
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.680
4lpk GDPGTPase KRas / 0.680
4lrw GDPGTPase KRas / 0.680
4x8o AP5Adenylate kinase / 0.680
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.679
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.679
3ea5 GDPGTP-binding nuclear protein Ran / 0.679
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
1xts GTPGTP-binding protein Rheb / 0.678
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.678
4dsu GDPGTPase KRas / 0.678
4pjj ADPUnconventional myosin-VI / 0.678
4qbi AP5Adenylate kinase / 0.678
2dpx GDPGTP-binding protein RAD / 0.677
4hi0 GDPUrease accessory protein UreG / 0.677
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.676
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.676
3l8y GNPGTPase HRas / 0.676
4iij GTPTubulin alpha-1B chain / 0.676
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.676
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.676
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.675
5itz GTPTubulin alpha-1B chain / 0.675
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.674
4hdq GNPRas-related protein Rap-1b / 0.674
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.674
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.673
3c41 ANPAmino acid ABC transporter / 0.673
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.673
1s3g AP5Adenylate kinase / 0.672
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.671
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.671
4d0l GSPRas-related protein Rab-11A / 0.671
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.671
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.671
1oix GDPRas-related protein Rab-11A / 0.670
3lbn GNPGTPase HRas / 0.670
4epw GDPGTPase KRas / 0.670
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.669
4o2l GTPGTP-binding protein Rheb / 0.669
3bc1 GNPRas-related protein Rab-27A / 0.668
4fu0 ADPD-alanine--D-alanine ligase / 0.668
2fe4 GDPRas-related protein Rab-6B / 0.667
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.666
4x8l AP5Adenylate kinase / 0.666
2ywv ADPPhosphoribosylaminoimidazole-succinocarboxamide synthase / 0.664
3m0e ATPTranscriptional regulator (NtrC family) / 0.664
3l1c ADPProtein claret segregational / 0.663
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.663
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.662
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.662
1svw GTPProbable GTP-binding protein EngB / 0.662
2w02 ATPAcsD / 0.662
4l9w GNPGTPase HRas / 0.662
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.662
4uj3 GNPRas-related protein Rab-11A / 0.662
1g16 GDPRas-related protein SEC4 / 0.661
3ryh GTPTubulin alpha chain / 0.661
1e0j ANPDNA primase/helicase 2.7.7 0.660
2vos ADPFolylpolyglutamate synthase / 0.660
3eg5 GNPCell division control protein 42 homolog / 0.660
1e4y AP5Adenylate kinase / 0.659
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.659
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.659
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.659
3nbx ADPATPase RavA 3.6.3 0.659
3lbi GNPGTPase HRas / 0.658
3rs7 GNPGTPase HRas / 0.658
4cdg ADPBloom syndrome protein 3.6.4.12 0.656
5cyo GDPSeptin-9 / 0.656
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.655
2jlr ANPGenome polyprotein 3.4.21.91 0.655
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.654
3oiw GNPGTPase HRas / 0.654
3rs0 GNPGTPase HRas / 0.654
4mit GTPRho-related protein racC / 0.654
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.653
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
3rs4 GNPGTPase HRas / 0.653
3rs5 GNPGTPase HRas / 0.653
1oyy AGSATP-dependent DNA helicase RecQ 3.6.4.12 0.652
5i4n ATPTyrosine-protein kinase JAK2 / 0.652
4dlv GNPGTPase HRas / 0.651
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.650