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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
4ww4 ADP RuvB-like helicase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ww4 ADPRuvB-like helicase / 1.212
2c9o ADPRuvB-like 1 3.6.4.12 0.932
3uk6 ADPRuvB-like 2 3.6.4.12 0.924
1w5s ADPORC1-type DNA replication protein 2 / 0.880
2xsz ATPRuvB-like 2 3.6.4.12 0.866
5fm6 ADPRuvB-like helicase / 0.864
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.831
2c9c ATPPsp operon transcriptional activator / 0.795
1fnn ADPORC1-type DNA replication protein / 0.790
2zr9 DTPProtein RecA / 0.790
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.782
1e4y AP5Adenylate kinase / 0.775
2c96 ATPPsp operon transcriptional activator / 0.769
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.768
2eck ADPAdenylate kinase / 0.764
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.759
1w5t ANPORC1-type DNA replication protein 2 / 0.757
4hse ADPChaperone protein ClpB / 0.752
3bbp GTPRas-related protein Rab-6A / 0.747
5fl3 ADPPili retraction protein PilT / 0.747
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.746
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.738
2gm1 ADPKinesin-like protein KIF11 / 0.737
2ql6 ADPNicotinamide riboside kinase 1 / 0.735
4iok ADPFormate--tetrahydrofolate ligase / 0.735
4tyq AP5Adenylate kinase / 0.733
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.732
1mma ADPMyosin-2 heavy chain / 0.731
1ny5 ADPTranscriptional regulator (NtrC family) / 0.731
4cf7 ADPAdenylate kinase / 0.729
1ake AP5Adenylate kinase / 0.727
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.727
4jjz ADPFormate--tetrahydrofolate ligase / 0.726
4qbh AP5Adenylate kinase / 0.726
2cea ADPATP-dependent zinc metalloprotease FtsH / 0.725
1fmw ATPMyosin-2 heavy chain / 0.724
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.720
3d8b ADPFidgetin-like protein 1 3.6.4 0.720
3kuc GDPRas-related protein Rap-1A / 0.719
1x1r GDPRas-related protein M-Ras / 0.718
3kkq GDPRas-related protein M-Ras / 0.717
4epx GDPGTPase KRas / 0.716
4ql3 GDPGTPase KRas / 0.716
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.715
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.715
1w5t ADPORC1-type DNA replication protein 2 / 0.713
1wdt GTPElongation factor G (EF-G-2) / 0.713
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.713
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.713
4o2r GDPGTP-binding protein Rheb / 0.713
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.712
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.712
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.712
1z0a GDPRas-related protein Rab-2A / 0.712
2gil GTPRas-related protein Rab-6A / 0.711
4qbi AP5Adenylate kinase / 0.710
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.709
2dft ADPShikimate kinase 2.7.1.71 0.706
5ftf ADPTPR domain protein / 0.706
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.705
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.704
1tu3 GNPRas-related protein Rab-5A / 0.704
3tqc ADPPantothenate kinase / 0.704
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.703
4qm6 GTPMetallophosphoesterase / 0.703
1xmv ADPProtein RecA / 0.702
4qbg AP5Adenylate kinase / 0.702
5bn3 ADPV-type ATP synthase alpha chain / 0.702
5bn3 ADPNEQ263 / 0.702
1e4v AP5Adenylate kinase / 0.701
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.701
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.700
1rrg GDPADP-ribosylation factor 1 / 0.700
1sdm ADPKinesin heavy chain-like protein / 0.700
1uad GNPRas-related protein Ral-A / 0.699
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.699
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.699
4x8o AP5Adenylate kinase / 0.698
4g0n GNPGTPase HRas / 0.697
1ii6 ADPKinesin-like protein KIF11 / 0.696
3pcr GTPADP-ribosylation factor 6 / 0.696
4lhv GDPRas-related protein Rab-8A / 0.696
4qnr ATPPsp operon transcriptional activator / 0.696
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.694
4g01 GDPRas-related protein RABF2b / 0.693
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.692
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.692
2zrj AGSProtein RecA / 0.691
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.691
2gcp GSPRho-related GTP-binding protein RhoC / 0.690
2uz3 TTPThymidine kinase / 0.690
3nbx ADPATPase RavA 3.6.3 0.690
3kud GDPGTPase HRas / 0.689
5ftc ADPTPR domain protein / 0.689
5hpy GDPTransforming protein RhoA / 0.689
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.688
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
2hld ANPATP synthase subunit alpha, mitochondrial / 0.688
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
3k1j ADPATP-dependent protease Lon / 0.688
4dxa GSPRas-related protein Rap-1b / 0.688
4mkh AP5Adenylate kinase / 0.688
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.687
1zbd GTPRas-related protein Rab-3A / 0.687
2ffq GSPRas-related protein Rab-6B / 0.687
1gwn GTPRho-related GTP-binding protein RhoE / 0.684
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.684
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
3mjh GTPRas-related protein Rab-5A / 0.684
2rgx AP5Adenylate kinase / 0.683
3law GNPRas-related protein Rab-7a / 0.683
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.683
4k81 GTPGTPase HRas / 0.683
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.681
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.681
4jsy GTPMetallophosphoesterase / 0.681
4o25 GTPGTP-binding protein Rheb / 0.681
1sxj ADPReplication factor C subunit 5 / 0.680
4l16 ADPFidgetin-like protein 1 3.6.4 0.680
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.679
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.677
2j5x GSPADP-ribosylation factor 6 / 0.677
4cdg ADPBloom syndrome protein 3.6.4.12 0.677
4lv6 GDPGTPase KRas / 0.677
1am4 GNPCell division control protein 42 homolog / 0.676
3t1t GDPProbable gliding protein mglA / 0.674
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.674
1z0f GDPRas-related protein Rab-14 / 0.673
2rgb GNPGTPase HRas / 0.673
3hpr AP5Adenylate kinase / 0.672
3oiu GNPGTPase HRas / 0.672
4dls GNPGTPase HRas / 0.672
4dlt GNPGTPase HRas / 0.672
4dlv GNPGTPase HRas / 0.672
3v4f GNPGTPase HRas / 0.671
5b2z GNPGTPase HRas / 0.671
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.670
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.670
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.669
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.669
3ref GDPRho family GTPase / 0.669
1zio AP5Adenylate kinase / 0.668
2bku GTPGTP-binding nuclear protein Ran / 0.668
4hdo GNPRas-related protein Rap-1b / 0.668
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.668
4gt8 ADPSensor protein VraS 2.7.13.3 0.667
5c46 GSPRas-related protein Rab-11A / 0.667
4cym GCPRas-related protein Rab-32 / 0.666
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.665
1g41 ADPATP-dependent protease ATPase subunit HslU / 0.664
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.664
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.664
4ap0 ADPKinesin-like protein KIF11 / 0.664
4mkf AP5Adenylate kinase / 0.664
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.663
3eg5 GNPCell division control protein 42 homolog / 0.663
3sop GDPNeuronal-specific septin-3 / 0.663
3tgp GNPGTPase HRas / 0.663
2fe4 GDPRas-related protein Rab-6B / 0.662
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.662
3myk ANPMyosin-2 heavy chain / 0.662
3x1w GDPRas-related protein Rap-1b / 0.662
4pfp ADPUnconventional myosin-VI / 0.662
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.662
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
4ldj GDPGTPase KRas / 0.661
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.660
4dso GSPGTPase KRas / 0.660
1qmg APXKetol-acid reductoisomerase, chloroplastic 1.1.1.86 0.659
4goj GNPADP-ribosylation factor-like protein 3 / 0.659
4l8g GDPGTPase KRas / 0.659
2bme GNPRas-related protein Rab-4A / 0.658
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.658
4dlx GNPGTPase HRas / 0.658
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.657
2zet GTPRas-related protein Rab-27B / 0.657
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.657
4asu ADPATP synthase subunit alpha, mitochondrial / 0.656
4d0l GSPRas-related protein Rab-11A / 0.656
4hdq GNPRas-related protein Rap-1b / 0.656
4o2l GTPGTP-binding protein Rheb / 0.656
4xvq GNPGTPase HRas / 0.656
4zca ADPKinesin-like protein KIF11 / 0.656
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.655
3kc1 2T6Fructose-1,6-bisphosphatase 1 3.1.3.11 0.655
3wyf GTPGTP-binding nuclear protein / 0.655
4v02 ATPSite-determining protein / 0.655
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.654
1mab ATPATP synthase subunit alpha, mitochondrial / 0.654
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.654
3t0z ATPHeat shock protein HSP 90-alpha / 0.654
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.654
1p3j AP5Adenylate kinase / 0.653
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.653
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
3a6p GTPGTP-binding nuclear protein Ran / 0.653
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.652
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
4i1v ADPDephospho-CoA kinase / 0.652
1d5c GDPGTPase (Rab6) / 0.651
1ibr GNPGTP-binding nuclear protein Ran / 0.651
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.651
4q03 GDPGTPase KRas / 0.651
1xts GTPGTP-binding protein Rheb / 0.650
3oes GNPGTPase RhebL1 / 0.650
3vtk ADPThymidine kinase / 0.650
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.650
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.650
4uj3 GNPRas-related protein Rab-11A / 0.650