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
4ww0 ADP ATP-dependent zinc metalloprotease FtsH

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 1.043
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.833
1w5s ADPORC1-type DNA replication protein 2 / 0.812
3k1j ADPATP-dependent protease Lon / 0.811
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.803
4ncl GDPEukaryotic translation initiation factor 5B / 0.798
5cyo GDPSeptin-9 / 0.784
2fl2 ADPKinesin-like protein KIF11 / 0.782
4ww4 ADPRuvB-like helicase / 0.782
4b7b ADPKinesin-like protein KIF11 / 0.780
2xae ADPKinesin-like protein KIF11 / 0.778
2x2r ADPKinesin-like protein KIF11 / 0.776
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.771
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.771
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.768
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.766
4lrw GDPGTPase KRas / 0.765
4d81 ADPAAA ATPase, central domain protein / 0.764
1xmv ADPProtein RecA / 0.761
2gm1 ADPKinesin-like protein KIF11 / 0.761
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.760
2x7e ADPKinesin-like protein KIF11 / 0.758
4luc GDPGTPase KRas / 0.757
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.757
3cob ADPKinesin heavy chain-like protein / 0.756
3kuc GDPRas-related protein Rap-1A / 0.756
1z0f GDPRas-related protein Rab-14 / 0.755
4dsu GDPGTPase KRas / 0.755
4o2r GDPGTP-binding protein Rheb / 0.755
1l8q ADPChromosomal replication initiator protein DnaA / 0.754
4q03 GDPGTPase KRas / 0.753
4a1z ADPKinesin-like protein KIF11 / 0.750
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.748
2pg2 ADPKinesin-like protein KIF11 / 0.748
2y65 ADPKinesin heavy chain / 0.748
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.748
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.747
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.747
4hse ADPChaperone protein ClpB / 0.746
2zfi ADPKinesin-like protein KIF1A / 0.745
4wa7 GDPGTPase KRas / 0.744
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.743
1sdm ADPKinesin heavy chain-like protein / 0.743
2fna ADPUncharacterized protein / 0.743
3l1c ADPProtein claret segregational / 0.742
4hi0 GDPUrease accessory protein UreG / 0.742
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.741
4pfp ADPUnconventional myosin-VI / 0.741
4pjj ADPUnconventional myosin-VI / 0.741
1sq5 ADPPantothenate kinase 2.7.1.33 0.740
2cea ADPATP-dependent zinc metalloprotease FtsH / 0.739
2dr3 ADPUPF0273 protein PH0284 / 0.739
4lv6 GDPGTPase KRas / 0.738
1z0a GDPRas-related protein Rab-2A / 0.737
1zbd GTPRas-related protein Rab-3A / 0.737
5aun ADPIron-sulfur cluster carrier protein / 0.737
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.736
2c9o ADPRuvB-like 1 3.6.4.12 0.736
2g1q ADPKinesin-like protein KIF11 / 0.736
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.736
2q2z ADPKinesin-like protein KIF11 / 0.735
3q5d GDPAtlastin-1 3.6.5 0.735
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.734
3ea5 GDPGTP-binding nuclear protein Ran / 0.733
4xsg GSPTransforming protein RhoA / 0.733
1w5t ADPORC1-type DNA replication protein 2 / 0.731
5fl3 ADPPili retraction protein PilT / 0.731
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.730
1yra GDPGPN-loop GTPase PAB0955 / 0.730
4itr GDPCell division control protein 42 homolog / 0.730
2ql6 ADPNicotinamide riboside kinase 1 / 0.729
2zrj AGSProtein RecA / 0.729
4g01 GDPRas-related protein RABF2b / 0.729
3r9i ADPSeptum site-determining protein MinD / 0.728
2xsz ATPRuvB-like 2 3.6.4.12 0.727
1wdt GTPElongation factor G (EF-G-2) / 0.726
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.726
4qxa GTPRas-related protein Rab-9A / 0.726
5bn3 ADPV-type ATP synthase alpha chain / 0.726
5bn3 ADPNEQ263 / 0.726
3bbp GTPRas-related protein Rab-6A / 0.725
1wbb ADPDNA mismatch repair protein MutS / 0.724
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.724
1jx2 ADPMyosin-2 heavy chain / 0.723
4o3m ADPBloom syndrome protein 3.6.4.12 0.723
4q02 GDPGTPase KRas / 0.723
3tqc ADPPantothenate kinase / 0.722
3x1w GDPRas-related protein Rap-1b / 0.722
4a51 ADPKinesin-like protein KIF11 / 0.722
4tq9 GDPGTPase KRas / 0.722
1ow3 GDPTransforming protein RhoA / 0.721
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.721
3kud GDPGTPase HRas / 0.721
1x1r GDPRas-related protein M-Ras / 0.720
3zia ATPATP synthase subunit alpha, mitochondrial / 0.720
2qen ADPWalker-Type ATPase / 0.719
3t1t GDPProbable gliding protein mglA / 0.719
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.718
1mma ADPMyosin-2 heavy chain / 0.718
4qos ADPPsp operon transcriptional activator / 0.718
4o25 GTPGTP-binding protein Rheb / 0.717
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.716
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.716
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.716
1fnn ADPORC1-type DNA replication protein / 0.715
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.715
2eck ADPAdenylate kinase / 0.715
3d8b ADPFidgetin-like protein 1 3.6.4 0.715
4kod ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.715
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.714
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.714
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.714
1oix GDPRas-related protein Rab-11A / 0.714
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.714
4xoi GTPTransforming protein RhoA / 0.714
1svl ADPLarge T antigen 3.6.4 0.713
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.713
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.713
2j5x GSPADP-ribosylation factor 6 / 0.713
3pcr GTPADP-ribosylation factor 6 / 0.713
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.713
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.713
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.712
3c41 ANPAmino acid ABC transporter / 0.711
4obe GDPGTPase KRas / 0.710
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.709
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.709
3tgp GNPGTPase HRas / 0.709
4epw GDPGTPase KRas / 0.709
5c46 GSPRas-related protein Rab-11A / 0.709
4iok ADPFormate--tetrahydrofolate ligase / 0.708
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.707
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.707
4ldj GDPGTPase KRas / 0.707
1b7t ADPMyosin heavy chain, striated muscle / 0.706
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.706
3l9h ADPKinesin-like protein KIF11 / 0.706
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.704
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.704
3ftq GNPSeptin-2 / 0.704
1ii6 ADPKinesin-like protein KIF11 / 0.703
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.703
4qbh AP5Adenylate kinase / 0.703
4y0v GDPADP-ribosylation factor 1, putative / 0.703
4ylg GDPADP-ribosylation factor 1, putative / 0.703
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.702
2bc9 GNPGuanylate-binding protein 1 / 0.701
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.701
4g0n GNPGTPase HRas / 0.701
3k3b ADPKinesin-like protein KIF11 / 0.700
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.700
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.699
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.699
1z0d GDPRas-related protein Rab-5C / 0.699
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.699
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.699
4x8o AP5Adenylate kinase / 0.699
1n6m ADPProtein claret segregational / 0.698
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.698
4pjk ADPMyosin-2 heavy chain / 0.698
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.697
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.697
5ftf ADPTPR domain protein / 0.697
1g6o ADPCag alpha / 0.696
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.696
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.696
3vhx GTPADP-ribosylation factor 6 / 0.696
4hdq GNPRas-related protein Rap-1b / 0.696
4jlo ADPAdenylate kinase / 0.696
4l8g GDPGTPase KRas / 0.696
4o2l GTPGTP-binding protein Rheb / 0.696
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.695
2rgg GNPGTPase HRas / 0.695
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.695
3oiu GNPGTPase HRas / 0.695
5ftc ADPTPR domain protein / 0.695
1s1c GNPTransforming protein RhoA / 0.694
1t91 GTPRas-related protein Rab-7a / 0.694
1uad GNPRas-related protein Ral-A / 0.694
1yrs ADPKinesin-like protein KIF11 / 0.694
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.694
1a2b GSPTransforming protein RhoA / 0.693
1ank ANPAdenylate kinase / 0.693
1w5t ANPORC1-type DNA replication protein 2 / 0.693
3qbt GNPRas-related protein Rab-8A / 0.693
4ap0 ADPKinesin-like protein KIF11 / 0.693
4epx GDPGTPase KRas / 0.693
2bku GTPGTP-binding nuclear protein Ran / 0.692
2l0x GDPGTP-binding protein Rheb / 0.692
3kkq GDPRas-related protein M-Ras / 0.692
4lpk GDPGTPase KRas / 0.692
1p9w ANPType II secretion system protein E / 0.691
3m0e ATPTranscriptional regulator (NtrC family) / 0.691
4dzz ADPPlasmid partitioning protein ParF / 0.691
1lfd GNPGTPase HRas / 0.690
1yzq GNPRas-related protein Rab-6A / 0.690
4ql3 GDPGTPase KRas / 0.690
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.690
4z54 GDPNeuronal-specific septin-3 / 0.690
1f5n GNPGuanylate-binding protein 1 / 0.689
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.689
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.688
4gp6 ADPMetallophosphoesterase / 0.688
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.686
4kvg GTPRas-related protein Rap-1A / 0.685
1ny5 ADPTranscriptional regulator (NtrC family) / 0.684
2cl6 CAGGTPase HRas / 0.684
2o8b ADPDNA mismatch repair protein Msh2 / 0.684
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.684
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.684
4cf7 ADPAdenylate kinase / 0.684
2ffq GSPRas-related protein Rab-6B / 0.683
4cym GCPRas-related protein Rab-32 / 0.683
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.682
3myk ANPMyosin-2 heavy chain / 0.682
3nbx ADPATPase RavA 3.6.3 0.682
1zc3 GNPRas-related protein Ral-A / 0.681
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.681
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
2uz3 TTPThymidine kinase / 0.681
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.681
4idn GNPAtlastin-1 3.6.5 0.681
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.679
3mjh GTPRas-related protein Rab-5A / 0.679
4ike ADPAdenylate kinase / 0.679
4xvq GNPGTPase HRas / 0.678
4yqf GDPSeptin-9 / 0.678
1kmq GNPTransforming protein RhoA / 0.677
1xts GTPGTP-binding protein Rheb / 0.677
1z6t ADPApoptotic protease-activating factor 1 / 0.677
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.677
3wyf GTPGTP-binding nuclear protein / 0.677
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.677
4zca ADPKinesin-like protein KIF11 / 0.677
5di3 GNPADP-ribosylation factor-like protein 3 / 0.677
1cxz GSPTransforming protein RhoA / 0.676
1g16 GDPRas-related protein SEC4 / 0.676
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.676
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.675
3a58 GNPGTP-binding protein RHO1 / 0.675
3pit GNPRas-related protein M-Ras / 0.673
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.672
4lhv GDPRas-related protein Rab-8A / 0.672
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.671
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.671
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.671
3ea0 ATPATPase, ParA family / 0.671
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.671
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.671
4dso GSPGTPase KRas / 0.671
5dif GNPGTP-binding nuclear protein Ran / 0.671
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.670
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.670
1e4v AP5Adenylate kinase / 0.669
3cph GDPRas-related protein SEC4 / 0.669
3k8y GNPGTPase HRas / 0.669
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.669
1gwn GTPRho-related GTP-binding protein RhoE / 0.668
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.668
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
1zc4 GNPRas-related protein Ral-A / 0.668
2ce2 GDPGTPase HRas / 0.668
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.668
3lbn GNPGTPase HRas / 0.668
4ihq ADPConserved Archaeal protein / 0.668
1rrg GDPADP-ribosylation factor 1 / 0.667
4jky ADPAdenylate kinase / 0.667
4l9w GNPGTPase HRas / 0.667
2vf7 ADPUvrABC system protein A / 0.666
3tso GNPRas-related protein Rab-25 / 0.666
4a28 ADPKinesin-like protein KIF11 / 0.666
4goj GNPADP-ribosylation factor-like protein 3 / 0.666
4jl6 ADPAdenylate kinase / 0.666
2bme GNPRas-related protein Rab-4A / 0.665
4asu ADPATP synthase subunit alpha, mitochondrial / 0.665
4d0l GSPRas-related protein Rab-11A / 0.665
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.665
1d5c GDPGTPase (Rab6) / 0.664
2ewv ADPTwitching motility protein PilT / 0.664
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.664
3ieu GDPGTPase Era / 0.664
4js0 GNPCell division control protein 42 homolog / 0.664
4lhw GNPRas-related protein Rab-8A / 0.664
1vg8 GNPRas-related protein Rab-7a / 0.663
1yu9 GNPRas-related protein Rab-4A / 0.663
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.663
3rab GNPRas-related protein Rab-3A / 0.663
4rkf GNPRas-related protein Rab-3 / 0.663
1n6l GTPRas-related protein Rab-5A / 0.662
1xms ANPProtein RecA / 0.662
1z2c GNPRho-related GTP-binding protein RhoC / 0.662
3tlx ADPAdenylate kinase 2 / 0.662
5bn4 ANPV-type ATP synthase alpha chain / 0.662
1tu3 GNPRas-related protein Rab-5A / 0.661
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.661
2c5l GTPGTPase HRas / 0.661
4hdo GNPRas-related protein Rap-1b / 0.661
4jld ADPAdenylate kinase / 0.661
4nh0 ATPESX secretion system protein EccC / 0.661
1a4r GNHCell division control protein 42 homolog / 0.660
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.660
3a6p GTPGTP-binding nuclear protein Ran / 0.660
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
4dls GNPGTPase HRas / 0.660
4iei ADPGene 2 protein / 0.660
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.659
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.659
4fvq ATPTyrosine-protein kinase JAK2 / 0.659
4jl5 ADPAdenylate kinase / 0.659
2rge GNPGTPase HRas / 0.658
1okk GCPSignal recognition particle protein / 0.657
1okk GCPSignal recognition particle receptor FtsY / 0.657
1wa5 GTPGTP-binding nuclear protein Ran / 0.657
2dpx GDPGTP-binding protein RAD / 0.657
2q2y ADPKinesin-like protein KIF11 / 0.657
4idp GNPAtlastin-1 3.6.5 0.657
4pk4 ADPUnconventional myosin-VI / 0.657
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
3aez GDPPantothenate kinase 2.7.1.33 0.656
3rs0 GNPGTPase HRas / 0.656
4l9s GDPGTPase HRas / 0.656
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.655
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
1piw NAPNADP-dependent alcohol dehydrogenase 6 1.1.1.2 0.655
1w7i ADPUnconventional myosin-Va / 0.655
2fe4 GDPRas-related protein Rab-6B / 0.655
4fvr ATPTyrosine-protein kinase JAK2 / 0.655
4c2u ANPDNA helicase / 0.654
3k9l GNPGTPase HRas / 0.653
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.652
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
5dha GNPGTP-binding nuclear protein Ran / 0.652
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.651
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.651
2q3f GNPRas-related GTP-binding protein D / 0.651
3bxz ADPProtein translocase subunit SecA / 0.651
3ddc GNPGTPase HRas / 0.651
3oiw GNPGTPase HRas / 0.651
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.651
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.650
4db1 ANPMyosin-7 / 0.650
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.650
5jlj GNPGTP-binding nuclear protein Ran / 0.650