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
4ymu ATP ABC-type polar amino acid transport system, ATPase component

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ymu ATPABC-type polar amino acid transport system, ATPase component / 1.081
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.814
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.788
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.782
3tlx ADPAdenylate kinase 2 / 0.780
4o2l GTPGTP-binding protein Rheb / 0.780
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.777
4dso GSPGTPase KRas / 0.776
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.775
1fmw ATPMyosin-2 heavy chain / 0.773
1wa5 GTPGTP-binding nuclear protein Ran / 0.769
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.767
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.763
4jl5 ADPAdenylate kinase / 0.763
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.762
4ike ADPAdenylate kinase / 0.762
1cxz GSPTransforming protein RhoA / 0.761
4jld ADPAdenylate kinase / 0.761
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.759
2eck ADPAdenylate kinase / 0.756
3ea5 GDPGTP-binding nuclear protein Ran / 0.756
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.750
4jl6 ADPAdenylate kinase / 0.748
4jlo ADPAdenylate kinase / 0.747
1d5c GDPGTPase (Rab6) / 0.746
1rrg GDPADP-ribosylation factor 1 / 0.746
3e5h GNPRas-related protein Rab-28 / 0.746
4jky ADPAdenylate kinase / 0.746
4mkh AP5Adenylate kinase / 0.746
4o2r GDPGTP-binding protein Rheb / 0.746
1ank ANPAdenylate kinase / 0.745
1l8q ADPChromosomal replication initiator protein DnaA / 0.745
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.745
1mma ADPMyosin-2 heavy chain / 0.742
2ql6 ADPNicotinamide riboside kinase 1 / 0.742
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.742
1t91 GTPRas-related protein Rab-7a / 0.741
3t1t GDPProbable gliding protein mglA / 0.741
4pjj ADPUnconventional myosin-VI / 0.741
2dr3 ADPUPF0273 protein PH0284 / 0.739
5fl3 ADPPili retraction protein PilT / 0.739
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.738
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.738
4dxa GSPRas-related protein Rap-1b / 0.738
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.737
4d0l GSPRas-related protein Rab-11A / 0.737
4xvq GNPGTPase HRas / 0.737
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.736
3mjh GTPRas-related protein Rab-5A / 0.736
2gm1 ADPKinesin-like protein KIF11 / 0.735
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.733
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.733
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.732
3kkq GDPRas-related protein M-Ras / 0.732
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.732
3tqc ADPPantothenate kinase / 0.731
4l8g GDPGTPase KRas / 0.731
2fe4 GDPRas-related protein Rab-6B / 0.730
4obe GDPGTPase KRas / 0.730
1fnn ADPORC1-type DNA replication protein / 0.729
1g6o ADPCag alpha / 0.728
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.728
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.728
4l9s GDPGTPase HRas / 0.728
4pfp ADPUnconventional myosin-VI / 0.728
1jx2 ADPMyosin-2 heavy chain / 0.727
1z6t ADPApoptotic protease-activating factor 1 / 0.727
4epw GDPGTPase KRas / 0.727
4q02 GDPGTPase KRas / 0.727
4ql3 GDPGTPase KRas / 0.727
1z0a GDPRas-related protein Rab-2A / 0.726
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.726
4epx GDPGTPase KRas / 0.726
4lv6 GDPGTPase KRas / 0.726
4q03 GDPGTPase KRas / 0.726
4tq9 GDPGTPase KRas / 0.726
1x1r GDPRas-related protein M-Ras / 0.725
1yra GDPGPN-loop GTPase PAB0955 / 0.725
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.725
3x1w GDPRas-related protein Rap-1b / 0.725
4ldj GDPGTPase KRas / 0.725
4wa7 GDPGTPase KRas / 0.725
2ce2 GDPGTPase HRas / 0.724
2dpx GDPGTP-binding protein RAD / 0.724
2ffq GSPRas-related protein Rab-6B / 0.724
3l1c ADPProtein claret segregational / 0.724
4qm6 GTPMetallophosphoesterase / 0.723
4qos ADPPsp operon transcriptional activator / 0.723
1g16 GDPRas-related protein SEC4 / 0.722
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.722
5cyo GDPSeptin-9 / 0.722
1sq5 ADPPantothenate kinase 2.7.1.33 0.721
3oes GNPGTPase RhebL1 / 0.721
1p9w ANPType II secretion system protein E / 0.720
4g01 GDPRas-related protein RABF2b / 0.720
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.720
1w5t ADPORC1-type DNA replication protein 2 / 0.719
1z2a GDPRas-related protein Rab-23 / 0.719
2zfi ADPKinesin-like protein KIF1A / 0.719
3ieu GDPGTPase Era / 0.719
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.719
4d81 ADPAAA ATPase, central domain protein / 0.719
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.719
4y0v GDPADP-ribosylation factor 1, putative / 0.719
4ylg GDPADP-ribosylation factor 1, putative / 0.719
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.718
3l9h ADPKinesin-like protein KIF11 / 0.718
1oix GDPRas-related protein Rab-11A / 0.717
3thy ADPDNA mismatch repair protein Msh2 / 0.717
2zrj AGSProtein RecA / 0.716
1ibr GNPGTP-binding nuclear protein Ran / 0.715
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.715
1kmq GNPTransforming protein RhoA / 0.714
4b7b ADPKinesin-like protein KIF11 / 0.714
3r9i ADPSeptum site-determining protein MinD / 0.713
3cph GDPRas-related protein SEC4 / 0.712
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.712
3kko GNPRas-related protein M-Ras / 0.712
5da9 AGSUncharacterized protein / 0.712
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.711
3pit GNPRas-related protein M-Ras / 0.711
4lpk GDPGTPase KRas / 0.711
2bbw GP5Adenylate kinase 4, mitochondrial / 0.710
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.710
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.710
1w5s ADPORC1-type DNA replication protein 2 / 0.709
3kud GDPGTPase HRas / 0.709
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.708
4hi0 GDPUrease accessory protein UreG / 0.708
4jjz ADPFormate--tetrahydrofolate ligase / 0.708
1gwn GTPRho-related GTP-binding protein RhoE / 0.707
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.707
4dsu GDPGTPase KRas / 0.707
4itr GDPCell division control protein 42 homolog / 0.707
4x8l AP5Adenylate kinase / 0.707
2zr9 DTPProtein RecA / 0.706
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.706
2xsz ATPRuvB-like 2 3.6.4.12 0.705
4qnr ATPPsp operon transcriptional activator / 0.705
1svl ADPLarge T antigen 3.6.4 0.704
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.702
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.700
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.699
4iok ADPFormate--tetrahydrofolate ligase / 0.699
4qbi AP5Adenylate kinase / 0.699
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
2rge GNPGTPase HRas / 0.698
1mmg AGSMyosin-2 heavy chain / 0.697
2fl2 ADPKinesin-like protein KIF11 / 0.697
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.697
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.696
2gcp GSPRho-related GTP-binding protein RhoC / 0.696
4i1v ADPDephospho-CoA kinase / 0.694
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.693
4jsy GTPMetallophosphoesterase / 0.693
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.693
1e4y AP5Adenylate kinase / 0.692
2c5l GTPGTPase HRas / 0.691
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.691
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.691
4luc GDPGTPase KRas / 0.691
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.690
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.690
2l0x GDPGTP-binding protein Rheb / 0.689
4yqf GDPSeptin-9 / 0.689
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.688
1kqm ANPMyosin heavy chain, striated muscle / 0.688
3ref GDPRho family GTPase / 0.688
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.687
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.687
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.685
4dls GNPGTPase HRas / 0.685
1xts GTPGTP-binding protein Rheb / 0.684
1z0d GDPRas-related protein Rab-5C / 0.684
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.684
1lfd GNPGTPase HRas / 0.683
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.683
1m7b GTPRho-related GTP-binding protein RhoE / 0.682
4dsn GCPGTPase KRas / 0.682
2c9c ATPPsp operon transcriptional activator / 0.681
1uad GNPRas-related protein Ral-A / 0.680
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.679
2vf7 ADPUvrABC system protein A / 0.678
3tnf GNPRas-related protein Rab-8A / 0.678
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.678
5c46 GSPRas-related protein Rab-11A / 0.678
1sxj ADPReplication factor C subunit 5 / 0.676
3pcr GTPADP-ribosylation factor 6 / 0.676
2whx ADPGenome polyprotein 3.4.21.91 0.675
3c41 ANPAmino acid ABC transporter / 0.675
3zfd ANPChromosome-associated kinesin KIF4 / 0.675
4xoi GTPTransforming protein RhoA / 0.675
2q3f GNPRas-related GTP-binding protein D / 0.674
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.674
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.674
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.671
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.671
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.670
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.670
2vos ADPFolylpolyglutamate synthase / 0.670
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.670
1b7t ADPMyosin heavy chain, striated muscle / 0.669
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.669
5b2z GNPGTPase HRas / 0.669
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.665
2zsa ADPPantothenate kinase 2.7.1.33 0.664
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.663
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
2r6g ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.663
4cf7 ADPAdenylate kinase / 0.663
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.662
1nsf ATPVesicle-fusing ATPase 3.6.4.6 0.661
1sxj AGSReplication factor C subunit 1 / 0.661
2bku GTPGTP-binding nuclear protein Ran / 0.661
4dlx GNPGTPase HRas / 0.661
4iei ADPGene 2 protein / 0.661
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.660
3w3z GTPGTP-binding nuclear protein Ran / 0.660
5ftc ADPTPR domain protein / 0.660
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.659
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.657
1xp8 AGSProtein RecA / 0.657
3i3s GNPGTPase HRas / 0.656
4fhp UTPTerminal uridylyltransferase cid1 / 0.656
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.655
3vhx GTPADP-ribosylation factor 6 / 0.655
4l16 ADPFidgetin-like protein 1 3.6.4 0.655
1a4r GNHCell division control protein 42 homolog / 0.654
1am4 GNPCell division control protein 42 homolog / 0.654
4nh0 ATPESX secretion system protein EccC / 0.654
1nly AGSCag alpha / 0.653
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.653
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.653
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.653
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.652
2cea ADPATP-dependent zinc metalloprotease FtsH / 0.652
4asu ADPATP synthase subunit alpha, mitochondrial / 0.652
5ftf ADPTPR domain protein / 0.652
3hqd ANPKinesin-like protein KIF11 / 0.651
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.651
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.651
4cym GCPRas-related protein Rab-32 / 0.651
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.651
1yzq GNPRas-related protein Rab-6A / 0.650
4uxj TTPThymidine kinase / 0.650