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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
2c9o ADP RuvB-like 1 3.6.4.12

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2c9o ADPRuvB-like 1 3.6.4.12 1.156
4ww4 ADPRuvB-like helicase / 0.932
2xsz ATPRuvB-like 2 3.6.4.12 0.897
1w5s ADPORC1-type DNA replication protein 2 / 0.865
5fm6 ADPRuvB-like helicase / 0.833
4x8l AP5Adenylate kinase / 0.823
1fnn ADPORC1-type DNA replication protein / 0.822
1w5t ADPORC1-type DNA replication protein 2 / 0.821
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.809
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.806
4qbh AP5Adenylate kinase / 0.806
3uk6 ADPRuvB-like 2 3.6.4.12 0.801
1l8q ADPChromosomal replication initiator protein DnaA / 0.795
2fna ADPUncharacterized protein / 0.795
4jl6 ADPAdenylate kinase / 0.791
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.790
4cf7 ADPAdenylate kinase / 0.781
1mma ADPMyosin-2 heavy chain / 0.780
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.778
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.775
2y65 ADPKinesin heavy chain / 0.775
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.775
3k1j ADPATP-dependent protease Lon / 0.775
2gm1 ADPKinesin-like protein KIF11 / 0.769
4pfp ADPUnconventional myosin-VI / 0.768
4pjk ADPMyosin-2 heavy chain / 0.768
1jx2 ADPMyosin-2 heavy chain / 0.767
4hse ADPChaperone protein ClpB / 0.761
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.760
4qbi AP5Adenylate kinase / 0.760
2j5x GSPADP-ribosylation factor 6 / 0.757
4b7b ADPKinesin-like protein KIF11 / 0.755
4jky ADPAdenylate kinase / 0.755
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.752
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.751
1p3j AP5Adenylate kinase / 0.750
4pk4 ADPUnconventional myosin-VI / 0.749
4xsg GSPTransforming protein RhoA / 0.748
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.746
4jl5 ADPAdenylate kinase / 0.746
4qm6 GTPMetallophosphoesterase / 0.746
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.745
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.744
4jlo ADPAdenylate kinase / 0.744
3m0e ATPTranscriptional regulator (NtrC family) / 0.742
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.740
2x2r ADPKinesin-like protein KIF11 / 0.740
2x7e ADPKinesin-like protein KIF11 / 0.740
4epw GDPGTPase KRas / 0.739
4lhv GDPRas-related protein Rab-8A / 0.739
1w5t ANPORC1-type DNA replication protein 2 / 0.738
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.737
4ldj GDPGTPase KRas / 0.736
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.736
1z0f GDPRas-related protein Rab-14 / 0.735
2q2z ADPKinesin-like protein KIF11 / 0.735
4dsu GDPGTPase KRas / 0.735
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.734
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.734
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.734
2zfi ADPKinesin-like protein KIF1A / 0.734
4mkf AP5Adenylate kinase / 0.734
2ffq GSPRas-related protein Rab-6B / 0.733
4ike ADPAdenylate kinase / 0.733
1wbb ADPDNA mismatch repair protein MutS / 0.732
2c5l GTPGTPase HRas / 0.732
4q03 GDPGTPase KRas / 0.732
1z0d GDPRas-related protein Rab-5C / 0.731
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.731
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.731
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.731
5fl3 ADPPili retraction protein PilT / 0.731
3kko GNPRas-related protein M-Ras / 0.730
4o2l GTPGTP-binding protein Rheb / 0.730
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.729
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.729
1z0a GDPRas-related protein Rab-2A / 0.728
4jsy GTPMetallophosphoesterase / 0.728
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.726
4x8o AP5Adenylate kinase / 0.726
3pit GNPRas-related protein M-Ras / 0.725
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.724
4pjj ADPUnconventional myosin-VI / 0.724
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.723
3mjh GTPRas-related protein Rab-5A / 0.723
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.722
2xae ADPKinesin-like protein KIF11 / 0.722
3a58 GNPGTP-binding protein RHO1 / 0.722
4lrw GDPGTPase KRas / 0.722
1wdt GTPElongation factor G (EF-G-2) / 0.720
3tqc ADPPantothenate kinase / 0.720
4hi0 GDPUrease accessory protein UreG / 0.720
4l8g GDPGTPase KRas / 0.719
4tyq AP5Adenylate kinase / 0.719
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.718
1wa5 GTPGTP-binding nuclear protein Ran / 0.718
5dif GNPGTP-binding nuclear protein Ran / 0.718
1ank ANPAdenylate kinase / 0.717
3t1t GDPProbable gliding protein mglA / 0.717
4jld ADPAdenylate kinase / 0.717
4l9s GDPGTPase HRas / 0.717
4qbg AP5Adenylate kinase / 0.717
5c46 GSPRas-related protein Rab-11A / 0.717
1x1r GDPRas-related protein M-Ras / 0.716
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.716
3oes GNPGTPase RhebL1 / 0.716
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.716
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.716
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.716
4q02 GDPGTPase KRas / 0.716
1sq5 ADPPantothenate kinase 2.7.1.33 0.715
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.715
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.715
4lv6 GDPGTPase KRas / 0.715
4ncl GDPEukaryotic translation initiation factor 5B / 0.715
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.714
3myk ANPMyosin-2 heavy chain / 0.714
3q5d GDPAtlastin-1 3.6.5 0.714
4g0n GNPGTPase HRas / 0.714
2eck ADPAdenylate kinase / 0.713
3ddc GNPGTPase HRas / 0.713
3tgp GNPGTPase HRas / 0.712
1ake AP5Adenylate kinase / 0.711
2rgb GNPGTPase HRas / 0.711
2rge GNPGTPase HRas / 0.711
2uyi ADPKinesin-like protein KIF11 / 0.711
3cph GDPRas-related protein SEC4 / 0.711
4dls GNPGTPase HRas / 0.711
4y0v GDPADP-ribosylation factor 1, putative / 0.711
4ylg GDPADP-ribosylation factor 1, putative / 0.711
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.710
4xvq GNPGTPase HRas / 0.710
1yra GDPGPN-loop GTPase PAB0955 / 0.708
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.707
1z6t ADPApoptotic protease-activating factor 1 / 0.706
2vf7 ADPUvrABC system protein A / 0.706
3r9i ADPSeptum site-determining protein MinD / 0.705
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.705
4ys0 ADPProtein translocase subunit SecA / 0.705
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.704
4z54 GDPNeuronal-specific septin-3 / 0.704
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.703
3x1w GDPRas-related protein Rap-1b / 0.703
1f5n GNPGuanylate-binding protein 1 / 0.702
1xtr GNPGTP-binding protein Rheb / 0.702
1rrg GDPADP-ribosylation factor 1 / 0.701
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.701
3ftq GNPSeptin-2 / 0.701
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.701
4d81 ADPAAA ATPase, central domain protein / 0.701
4o25 GTPGTP-binding protein Rheb / 0.701
4ql3 GDPGTPase KRas / 0.701
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.701
2bc9 GNPGuanylate-binding protein 1 / 0.700
3hpq AP5Adenylate kinase / 0.700
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.700
4jjz ADPFormate--tetrahydrofolate ligase / 0.700
1e4v AP5Adenylate kinase / 0.699
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.699
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.699
4dso GSPGTPase KRas / 0.699
4epx GDPGTPase KRas / 0.699
5di3 GNPADP-ribosylation factor-like protein 3 / 0.699
1lfd GNPGTPase HRas / 0.698
1tu3 GNPRas-related protein Rab-5A / 0.698
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.698
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.697
2gcp GSPRho-related GTP-binding protein RhoC / 0.697
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.697
2rgg GNPGTPase HRas / 0.697
3d8b ADPFidgetin-like protein 1 3.6.4 0.697
3qbt GNPRas-related protein Rab-8A / 0.696
3vhx GTPADP-ribosylation factor 6 / 0.696
4yqf GDPSeptin-9 / 0.696
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.695
1zc3 GNPRas-related protein Ral-A / 0.695
2bme GNPRas-related protein Rab-4A / 0.695
2fe4 GDPRas-related protein Rab-6B / 0.695
3l9h ADPKinesin-like protein KIF11 / 0.695
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.695
4dlt GNPGTPase HRas / 0.695
1yu9 GNPRas-related protein Rab-4A / 0.694
2osb AP5Adenylate kinase / 0.694
4l9w GNPGTPase HRas / 0.694
3cob ADPKinesin heavy chain-like protein / 0.693
4goj GNPADP-ribosylation factor-like protein 3 / 0.693
4iok ADPFormate--tetrahydrofolate ligase / 0.693
4idn GNPAtlastin-1 3.6.5 0.692
4lj7 MNTChaperone protein ClpB / 0.692
4oi2 ADPProtein clpf-1 / 0.692
1kmq GNPTransforming protein RhoA / 0.691
2rgx AP5Adenylate kinase / 0.691
4g01 GDPRas-related protein RABF2b / 0.691
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.690
3bbp GTPRas-related protein Rab-6A / 0.690
3hpr AP5Adenylate kinase / 0.690
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.690
4a51 ADPKinesin-like protein KIF11 / 0.690
4idp GNPAtlastin-1 3.6.5 0.690
1uad GNPRas-related protein Ral-A / 0.689
5bn3 ADPV-type ATP synthase alpha chain / 0.689
5bn3 ADPNEQ263 / 0.689
2zrj AGSProtein RecA / 0.688
3dzd ADPTranscriptional regulator (NtrC family) / 0.688
3tkl GTPRas-related protein Rab-1A / 0.688
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.688
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.687
1g6o ADPCag alpha / 0.686
1ny5 ADPTranscriptional regulator (NtrC family) / 0.686
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.686
2ql6 ADPNicotinamide riboside kinase 1 / 0.685
3kud GDPGTPase HRas / 0.685
4o2r GDPGTP-binding protein Rheb / 0.685
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.684
2pg2 ADPKinesin-like protein KIF11 / 0.683
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.683
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.683
4wa7 GDPGTPase KRas / 0.683
1gwn GTPRho-related GTP-binding protein RhoE / 0.682
2ce2 GDPGTPase HRas / 0.682
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.682
3kuc GDPRas-related protein Rap-1A / 0.682
3ea5 GDPGTP-binding nuclear protein Ran / 0.681
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.681
1kqm ANPMyosin heavy chain, striated muscle / 0.680
2d7d ADPUvrABC system protein B / 0.679
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
3oiu GNPGTPase HRas / 0.679
4nh0 ATPESX secretion system protein EccC / 0.679
4qos ADPPsp operon transcriptional activator / 0.679
3v4f GNPGTPase HRas / 0.678
4lhw GNPRas-related protein Rab-8A / 0.678
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.678
1b7t ADPMyosin heavy chain, striated muscle / 0.677
1n6l GTPRas-related protein Rab-5A / 0.677
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.676
1z2a GDPRas-related protein Rab-23 / 0.676
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.676
4js0 GNPCell division control protein 42 homolog / 0.676
4obe GDPGTPase KRas / 0.676
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.676
5aun ADPIron-sulfur cluster carrier protein / 0.676
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.676
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.675
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.675
2nmv ADPUvrABC system protein B / 0.675
2vor ACPFolylpolyglutamate synthase / 0.675
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.675
1p9w ANPType II secretion system protein E / 0.674
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.674
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.672
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
1am4 GNPCell division control protein 42 homolog / 0.671
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.671
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.671
3w3z GTPGTP-binding nuclear protein Ran / 0.671
4c30 ANPDNA helicase / 0.671
5fm7 ADPRuvB-like helicase / 0.671
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.670
3zfd ANPChromosome-associated kinesin KIF4 / 0.670
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.669
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.668
4ihq ADPConserved Archaeal protein / 0.668
4ohx ADPProtein clpf-1 / 0.668
4uj3 GNPRas-related protein Rab-11A / 0.668
5hpy GDPTransforming protein RhoA / 0.668
5l3s GNPSignal recognition particle receptor FtsY / 0.668
1g16 GDPRas-related protein SEC4 / 0.667
3a6p GTPGTP-binding nuclear protein Ran / 0.666
3x1z GNPRas-related protein Rap-1b / 0.666
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.665
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
4a28 ADPKinesin-like protein KIF11 / 0.665
4hdo GNPRas-related protein Rap-1b / 0.665
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.664
3jvv ACPTwitching mobility protein / 0.664
3tso GNPRas-related protein Rab-25 / 0.664
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.663
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.663
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.663
3rab GNPRas-related protein Rab-3A / 0.663
4k81 GTPGTPase HRas / 0.663
5dha GNPGTP-binding nuclear protein Ran / 0.663
3ieu GDPGTPase Era / 0.662
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.662
3oiv GNPGTPase HRas / 0.662
3ref GDPRho family GTPase / 0.662
3sop GDPNeuronal-specific septin-3 / 0.662
1sdm ADPKinesin heavy chain-like protein / 0.661
3pfd FDAAcyl-CoA dehydrogenase FadE25 / 0.661
3r9x GNPGTPase Era / 0.661
4hdq GNPRas-related protein Rap-1b / 0.661
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.660
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.660
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.660
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.659
2dft ADPShikimate kinase 2.7.1.71 0.659
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.658
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.658
1xts GTPGTP-binding protein Rheb / 0.658
3eg5 GNPCell division control protein 42 homolog / 0.658
1ky2 GNPGTP-binding protein YPT7 / 0.657
3k3b ADPKinesin-like protein KIF11 / 0.657
4lpk GDPGTPase KRas / 0.657
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.656
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.656
3oiw GNPGTPase HRas / 0.656
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.656
4iei ADPGene 2 protein / 0.656
4ol0 GTPGTP-binding nuclear protein Ran / 0.656
1k5d GNPGTP-binding nuclear protein Ran / 0.655
2c96 ATPPsp operon transcriptional activator / 0.655
3pcr GTPADP-ribosylation factor 6 / 0.655
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.655
2hld ANPATP synthase subunit alpha, mitochondrial / 0.654
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.654
2qen ADPWalker-Type ATPase / 0.654
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.654
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.654
4tq9 GDPGTPase KRas / 0.654
1w7i ADPUnconventional myosin-Va / 0.653
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.653
4d0l GSPRas-related protein Rab-11A / 0.653
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.652
4bmz MTAAminodeoxyfutalosine nucleosidase / 0.652
4l16 ADPFidgetin-like protein 1 3.6.4 0.652
1foa UD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase 2.4.1.101 0.651
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.651
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.651
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.651
4gp6 ADPMetallophosphoesterase / 0.651
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
1mmg AGSMyosin-2 heavy chain / 0.650
3k9l GNPGTPase HRas / 0.650
5cyo GDPSeptin-9 / 0.650
5ftf ADPTPR domain protein / 0.650