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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
3i5x ANP ATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 1.256
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 1.232
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 1.175
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 1.010
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.890
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.884
1f5n GNPGuanylate-binding protein 1 / 0.804
4c30 ANPDNA helicase / 0.799
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.797
3wyf GTPGTP-binding nuclear protein / 0.795
1fmw ATPMyosin-2 heavy chain / 0.789
1mmg AGSMyosin-2 heavy chain / 0.786
4idp GNPAtlastin-1 3.6.5 0.786
1zc3 GNPRas-related protein Ral-A / 0.785
3rs4 GNPGTPase HRas / 0.784
3rs5 GNPGTPase HRas / 0.784
4dlv GNPGTPase HRas / 0.784
4hdo GNPRas-related protein Rap-1b / 0.784
3rs0 GNPGTPase HRas / 0.783
3rs7 GNPGTPase HRas / 0.783
3rsl GNPGTPase HRas / 0.783
4dlt GNPGTPase HRas / 0.783
4l9w GNPGTPase HRas / 0.783
2rgc GNPGTPase HRas / 0.782
4dlx GNPGTPase HRas / 0.782
3rab GNPRas-related protein Rab-3A / 0.779
3zfd ANPChromosome-associated kinesin KIF4 / 0.779
1zc4 GNPRas-related protein Ral-A / 0.777
4rkf GNPRas-related protein Rab-3 / 0.771
5dif GNPGTP-binding nuclear protein Ran / 0.771
2c5l GTPGTPase HRas / 0.770
3oiu GNPGTPase HRas / 0.769
3v4f GNPGTPase HRas / 0.769
4dlz GNPGTPase HRas / 0.768
4idn GNPAtlastin-1 3.6.5 0.768
3b1x GNPFerrous iron transport protein B / 0.767
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.767
3i3s GNPGTPase HRas / 0.766
3k8y GNPGTPase HRas / 0.766
3w3z GTPGTP-binding nuclear protein Ran / 0.766
3x1z GNPRas-related protein Rap-1b / 0.766
2jlr ANPGenome polyprotein 3.4.21.91 0.765
3oiw GNPGTPase HRas / 0.765
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.764
3oiv GNPGTPase HRas / 0.764
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.763
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.762
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.762
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.762
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.761
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.761
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.756
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.755
2rgb GNPGTPase HRas / 0.754
4uj3 GNPRas-related protein Rab-11A / 0.754
3lbn GNPGTPase HRas / 0.753
3l8y GNPGTPase HRas / 0.752
4dso GSPGTPase KRas / 0.752
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.752
1yu9 GNPRas-related protein Rab-4A / 0.751
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.751
4dls GNPGTPase HRas / 0.751
4lhw GNPRas-related protein Rab-8A / 0.751
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.750
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.750
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.750
3ddc GNPGTPase HRas / 0.750
3pit GNPRas-related protein M-Ras / 0.749
3tso GNPRas-related protein Rab-25 / 0.748
2bku GTPGTP-binding nuclear protein Ran / 0.747
4c2u ANPDNA helicase / 0.747
4z54 GDPNeuronal-specific septin-3 / 0.747
4qxa GTPRas-related protein Rab-9A / 0.746
4pfp ADPUnconventional myosin-VI / 0.745
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.744
1jx2 ADPMyosin-2 heavy chain / 0.744
1mma ADPMyosin-2 heavy chain / 0.744
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.743
1wa5 GTPGTP-binding nuclear protein Ran / 0.743
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.743
1kmq GNPTransforming protein RhoA / 0.741
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.741
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.741
4js0 GNPCell division control protein 42 homolog / 0.741
5l3s GNPSignal recognition particle receptor FtsY / 0.739
1tu3 GNPRas-related protein Rab-5A / 0.738
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.738
3ftq GNPSeptin-2 / 0.738
3lbi GNPGTPase HRas / 0.738
3kko GNPRas-related protein M-Ras / 0.736
3mjh GTPRas-related protein Rab-5A / 0.736
2rge GNPGTPase HRas / 0.735
2rgg GNPGTPase HRas / 0.735
3lbh GNPGTPase HRas / 0.735
2j7p GNPSignal recognition particle protein / 0.733
2j7p GNPSignal recognition particle receptor FtsY / 0.733
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.733
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.731
4nyi GNPGTPase HRas / 0.730
3q5d GDPAtlastin-1 3.6.5 0.728
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.727
4pjj ADPUnconventional myosin-VI / 0.726
5dha GNPGTP-binding nuclear protein Ran / 0.725
1m7b GTPRho-related GTP-binding protein RhoE / 0.724
1wdt GTPElongation factor G (EF-G-2) / 0.724
3qbt GNPRas-related protein Rab-8A / 0.724
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.723
4yqf GDPSeptin-9 / 0.722
3k9l GNPGTPase HRas / 0.721
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.720
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.720
1xtr GNPGTP-binding protein Rheb / 0.720
1yzq GNPRas-related protein Rab-6A / 0.720
2gcp GSPRho-related GTP-binding protein RhoC / 0.720
2q3f GNPRas-related GTP-binding protein D / 0.718
3zia ATPATP synthase subunit alpha, mitochondrial / 0.718
4k81 GTPGTPase HRas / 0.717
3bc1 GNPRas-related protein Rab-27A / 0.716
3oes GNPGTPase RhebL1 / 0.716
3vhx GTPADP-ribosylation factor 6 / 0.716
4mit GTPRho-related protein racC / 0.716
5bn3 ADPV-type ATP synthase alpha chain / 0.716
5bn3 ADPNEQ263 / 0.716
2c9o ADPRuvB-like 1 3.6.4.12 0.715
2cl6 CAGGTPase HRas / 0.715
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.715
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.713
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.713
4xvu ATPATPase GET3 / 0.713
3ea5 GDPGTP-binding nuclear protein Ran / 0.711
3tgp GNPGTPase HRas / 0.711
4lhv GDPRas-related protein Rab-8A / 0.711
1oyy AGSATP-dependent DNA helicase RecQ 3.6.4.12 0.710
5aun ADPIron-sulfur cluster carrier protein / 0.710
1fnn ADPORC1-type DNA replication protein / 0.709
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.708
4pk4 ADPUnconventional myosin-VI / 0.707
1sxj AGSReplication factor C subunit 1 / 0.704
2ffq GSPRas-related protein Rab-6B / 0.704
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.702
4xvq GNPGTPase HRas / 0.702
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.700
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.700
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.699
4xvr GNPGTPase HRas / 0.699
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.698
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.698
4wa7 GDPGTPase KRas / 0.698
1ibr GNPGTP-binding nuclear protein Ran / 0.697
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.696
4dsu GDPGTPase KRas / 0.696
1ow3 GDPTransforming protein RhoA / 0.695
2rgx AP5Adenylate kinase / 0.694
1kqm ANPMyosin heavy chain, striated muscle / 0.693
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.693
4ql3 GDPGTPase KRas / 0.693
4ys0 ADPProtein translocase subunit SecA / 0.693
1z2a GDPRas-related protein Rab-23 / 0.692
1w5s ADPORC1-type DNA replication protein 2 / 0.691
1z0d GDPRas-related protein Rab-5C / 0.691
2fg5 GNPRas-related protein Rab-31 / 0.691
4dxa GSPRas-related protein Rap-1b / 0.691
1s1c GNPTransforming protein RhoA / 0.690
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.690
1cxz GSPTransforming protein RhoA / 0.689
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.689
3a6p GTPGTP-binding nuclear protein Ran / 0.688
3tnf GNPRas-related protein Rab-8A / 0.688
4dvg GSPRho family GTPase / 0.688
4mkf AP5Adenylate kinase / 0.688
5di3 GNPADP-ribosylation factor-like protein 3 / 0.687
1uad GNPRas-related protein Ral-A / 0.686
2dpx GDPGTP-binding protein RAD / 0.686
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.685
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.683
2j5x GSPADP-ribosylation factor 6 / 0.683
3sop GDPNeuronal-specific septin-3 / 0.683
1nly AGSCag alpha / 0.682
2xsz ATPRuvB-like 2 3.6.4.12 0.682
4l8g GDPGTPase KRas / 0.682
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.681
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.681
1ank ANPAdenylate kinase / 0.680
1oix GDPRas-related protein Rab-11A / 0.680
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.679
4epw GDPGTPase KRas / 0.679
4l9s GDPGTPase HRas / 0.679
5cyo GDPSeptin-9 / 0.679
2c96 ATPPsp operon transcriptional activator / 0.678
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.678
3bbp GTPRas-related protein Rab-6A / 0.677
3pcr GTPADP-ribosylation factor 6 / 0.677
1d5c GDPGTPase (Rab6) / 0.676
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.676
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.676
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
2ce2 GDPGTPase HRas / 0.675
4lpk GDPGTPase KRas / 0.675
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.673
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.673
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.673
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.673
2pui ADPMethylthioribose kinase 2.7.1.100 0.673
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.673
3fkq ATPNtrC-like two-domain protein / 0.672
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.672
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.671
2eck ADPAdenylate kinase / 0.670
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.669
4o3m ADPBloom syndrome protein 3.6.4.12 0.669
1p3j AP5Adenylate kinase / 0.668
2gm1 ADPKinesin-like protein KIF11 / 0.667
2zfi ADPKinesin-like protein KIF1A / 0.667
3kfl ME8Putative methionyl-tRNA synthetase / 0.667
4ceg ADPAurora kinase A 2.7.11.1 0.667
4epx GDPGTPase KRas / 0.667
4lv6 GDPGTPase KRas / 0.667
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.666
4pjk ADPMyosin-2 heavy chain / 0.666
1z0f GDPRas-related protein Rab-14 / 0.665
3e5h GNPRas-related protein Rab-28 / 0.665
4fvq ATPTyrosine-protein kinase JAK2 / 0.665
4ihq ADPConserved Archaeal protein / 0.665
4ike ADPAdenylate kinase / 0.665
5ftc ADPTPR domain protein / 0.665
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.664
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.664
2hld ANPATP synthase subunit alpha, mitochondrial / 0.664
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.664
4dee ADPAurora kinase A 2.7.11.1 0.664
4hdq GNPRas-related protein Rap-1b / 0.664
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.664
4df8 0L4DNA polymerase I, thermostable 2.7.7.7 0.663
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.662
1svm ATPLarge T antigen 3.6.4 0.661
3ref GDPRho family GTPase / 0.661
1ss9 UPFLgtC / 0.660
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.660
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.660
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
4d0l GSPRas-related protein Rab-11A / 0.660
4itr GDPCell division control protein 42 homolog / 0.660
4jl6 ADPAdenylate kinase / 0.660
4nh0 ATPESX secretion system protein EccC / 0.660
4tx9 AMZPhosphoribosyl isomerase A / 0.660
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.659
3au2 DGTDNA polymerase beta family (X family) / 0.659
3bxz ADPProtein translocase subunit SecA / 0.659
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.658
1n2g APCPantothenate synthetase 6.3.2.1 0.657
2zr9 DTPProtein RecA / 0.657
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.657
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.657
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.656
3tjz GNPADP-ribosylation factor 1 / 0.656
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.655
1zbd GTPRas-related protein Rab-3A / 0.654
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.654
3q9l ATPSeptum site-determining protein MinD / 0.654
1svl ADPLarge T antigen 3.6.4 0.653
2uz3 TTPThymidine kinase / 0.652
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.652
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.651
3rye UNRFarnesyl pyrophosphate synthase 2.5.1.10 0.651
4jld ADPAdenylate kinase / 0.651
4tq9 GDPGTPase KRas / 0.651
1zdg UPGGlycogenin-1 2.4.1.186 0.650
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.650
3sup DCPDNA-directed DNA polymerase / 0.650
4asu ADPATP synthase subunit alpha, mitochondrial / 0.650