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
2dr3 ADP UPF0273 protein PH0284

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2dr3 ADPUPF0273 protein PH0284 / 0.999
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.834
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.791
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.785
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.770
2zts ADPUncharacterized protein / 0.763
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.761
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.761
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.761
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.761
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.757
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.757
3l9h ADPKinesin-like protein KIF11 / 0.757
4d81 ADPAAA ATPase, central domain protein / 0.756
2uyi ADPKinesin-like protein KIF11 / 0.755
2xae ADPKinesin-like protein KIF11 / 0.754
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.753
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.753
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.752
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.751
4lrw GDPGTPase KRas / 0.750
1l8q ADPChromosomal replication initiator protein DnaA / 0.749
3cob ADPKinesin heavy chain-like protein / 0.749
4hse ADPChaperone protein ClpB / 0.748
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.744
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.743
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.743
1sdm ADPKinesin heavy chain-like protein / 0.742
1xmv ADPProtein RecA / 0.742
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.741
3d8b ADPFidgetin-like protein 1 3.6.4 0.741
4pjk ADPMyosin-2 heavy chain / 0.741
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.741
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.741
1fnn ADPORC1-type DNA replication protein / 0.740
2pg2 ADPKinesin-like protein KIF11 / 0.740
4b7b ADPKinesin-like protein KIF11 / 0.740
4z54 GDPNeuronal-specific septin-3 / 0.740
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.739
2x2r ADPKinesin-like protein KIF11 / 0.739
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.739
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.739
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.737
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.737
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.737
2zfi ADPKinesin-like protein KIF1A / 0.737
3cf0 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.736
3vhx GTPADP-ribosylation factor 6 / 0.736
4pk4 ADPUnconventional myosin-VI / 0.736
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.735
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.734
4dso GSPGTPase KRas / 0.734
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.733
2bku GTPGTP-binding nuclear protein Ran / 0.732
2gm1 ADPKinesin-like protein KIF11 / 0.732
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.732
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.732
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.731
4a1z ADPKinesin-like protein KIF11 / 0.731
1wbb ADPDNA mismatch repair protein MutS / 0.730
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.730
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.729
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.729
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.728
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.728
1w5t ADPORC1-type DNA replication protein 2 / 0.728
2qen ADPWalker-Type ATPase / 0.728
4hi0 GDPUrease accessory protein UreG / 0.726
5cyo GDPSeptin-9 / 0.726
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.725
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.724
3ea5 GDPGTP-binding nuclear protein Ran / 0.724
4pjj ADPUnconventional myosin-VI / 0.724
2y65 ADPKinesin heavy chain / 0.723
2zrj AGSProtein RecA / 0.722
4jky ADPAdenylate kinase / 0.722
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.721
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.721
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.720
4cym GCPRas-related protein Rab-32 / 0.720
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.720
3a6p GTPGTP-binding nuclear protein Ran / 0.719
2fl2 ADPKinesin-like protein KIF11 / 0.718
2x7e ADPKinesin-like protein KIF11 / 0.718
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.718
3tlx ADPAdenylate kinase 2 / 0.718
4l8g GDPGTPase KRas / 0.718
1tu3 GNPRas-related protein Rab-5A / 0.717
2fna ADPUncharacterized protein / 0.717
3c41 ANPAmino acid ABC transporter / 0.717
4a51 ADPKinesin-like protein KIF11 / 0.717
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.716
2ql6 ADPNicotinamide riboside kinase 1 / 0.716
4l9s GDPGTPase HRas / 0.716
4obe GDPGTPase KRas / 0.716
4epw GDPGTPase KRas / 0.715
4lpk GDPGTPase KRas / 0.715
4ncl GDPEukaryotic translation initiation factor 5B / 0.715
1z0f GDPRas-related protein Rab-14 / 0.714
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.714
3kkq GDPRas-related protein M-Ras / 0.713
3q5d GDPAtlastin-1 3.6.5 0.713
4ldj GDPGTPase KRas / 0.713
4o2r GDPGTP-binding protein Rheb / 0.713
4tq9 GDPGTPase KRas / 0.713
1sq5 ADPPantothenate kinase 2.7.1.33 0.712
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.712
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.711
4luc GDPGTPase KRas / 0.711
1z0d GDPRas-related protein Rab-5C / 0.710
1b7t ADPMyosin heavy chain, striated muscle / 0.709
1z2a GDPRas-related protein Rab-23 / 0.709
3bbp GTPRas-related protein Rab-6A / 0.709
3ieu GDPGTPase Era / 0.708
4pfp ADPUnconventional myosin-VI / 0.708
2cl6 CAGGTPase HRas / 0.707
4iei ADPGene 2 protein / 0.707
1jx2 ADPMyosin-2 heavy chain / 0.706
1w5t ANPORC1-type DNA replication protein 2 / 0.706
4dxa GSPRas-related protein Rap-1b / 0.706
1g16 GDPRas-related protein SEC4 / 0.705
1rrg GDPADP-ribosylation factor 1 / 0.705
1z0a GDPRas-related protein Rab-2A / 0.705
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.705
3k1j ADPATP-dependent protease Lon / 0.705
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.705
5ftc ADPTPR domain protein / 0.705
5dif GNPGTP-binding nuclear protein Ran / 0.704
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.703
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.701
3kud GDPGTPase HRas / 0.701
1svm ATPLarge T antigen 3.6.4 0.700
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.700
3law GNPRas-related protein Rab-7a / 0.700
3qbv GDPCell division control protein 42 homolog / 0.700
4asu ADPATP synthase subunit alpha, mitochondrial / 0.700
4o2l GTPGTP-binding protein Rheb / 0.700
1yrs ADPKinesin-like protein KIF11 / 0.699
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.699
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.699
4l9w GNPGTPase HRas / 0.699
5dha GNPGTP-binding nuclear protein Ran / 0.699
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.698
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.698
3l1c ADPProtein claret segregational / 0.698
4jlo ADPAdenylate kinase / 0.698
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.697
4ap0 ADPKinesin-like protein KIF11 / 0.697
4ihq ADPConserved Archaeal protein / 0.697
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.696
1gwn GTPRho-related GTP-binding protein RhoE / 0.695
4dzz ADPPlasmid partitioning protein ParF / 0.695
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.694
1yra GDPGPN-loop GTPase PAB0955 / 0.694
3kuc GDPRas-related protein Rap-1A / 0.694
4q02 GDPGTPase KRas / 0.694
1d5c GDPGTPase (Rab6) / 0.693
1ow3 GDPTransforming protein RhoA / 0.693
1svl ADPLarge T antigen 3.6.4 0.693
4jl5 ADPAdenylate kinase / 0.693
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.693
1g6o ADPCag alpha / 0.692
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.692
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.692
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.692
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.691
1xp8 AGSProtein RecA / 0.691
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.691
3tjz GNPADP-ribosylation factor 1 / 0.691
4lv6 GDPGTPase KRas / 0.690
4y0v GDPADP-ribosylation factor 1, putative / 0.690
4ylg GDPADP-ribosylation factor 1, putative / 0.690
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.689
2l0x GDPGTP-binding protein Rheb / 0.689
3x1w GDPRas-related protein Rap-1b / 0.689
4wa7 GDPGTPase KRas / 0.689
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.688
3dvl ATPCircadian clock protein kinase KaiC 2.7.11.1 0.688
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.688
4dsu GDPGTPase KRas / 0.687
4yqf GDPSeptin-9 / 0.687
1f5n GNPGuanylate-binding protein 1 / 0.686
2fe4 GDPRas-related protein Rab-6B / 0.686
2jlr ANPGenome polyprotein 3.4.21.91 0.686
4i1v ADPDephospho-CoA kinase / 0.686
5jlj GNPGTP-binding nuclear protein Ran / 0.686
1x1r GDPRas-related protein M-Ras / 0.685
3cph GDPRas-related protein SEC4 / 0.685
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.685
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.684
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.684
4qbh AP5Adenylate kinase / 0.684
4ql3 GDPGTPase KRas / 0.684
2uz3 TTPThymidine kinase / 0.683
3myk ANPMyosin-2 heavy chain / 0.683
4uj3 GNPRas-related protein Rab-11A / 0.683
2g1q ADPKinesin-like protein KIF11 / 0.682
2o8b ADPDNA mismatch repair protein Msh2 / 0.682
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.682
3ref GDPRho family GTPase / 0.681
3tqc ADPPantothenate kinase / 0.681
4cf7 ADPAdenylate kinase / 0.681
2cea ADPATP-dependent zinc metalloprotease FtsH / 0.680
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.679
1k5d GNPGTP-binding nuclear protein Ran / 0.679
1mma ADPMyosin-2 heavy chain / 0.677
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.677
2ce2 GDPGTPase HRas / 0.676
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.676
4jld ADPAdenylate kinase / 0.676
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.676
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.675
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.675
2dpx GDPGTP-binding protein RAD / 0.675
4uxj TTPThymidine kinase / 0.675
4iok ADPFormate--tetrahydrofolate ligase / 0.674
3pcr GTPADP-ribosylation factor 6 / 0.673
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.673
4a28 ADPKinesin-like protein KIF11 / 0.673
4q03 GDPGTPase KRas / 0.673
1lfd GNPGTPase HRas / 0.672
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.672
4epx GDPGTPase KRas / 0.672
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.672
4o25 GTPGTP-binding protein Rheb / 0.672
4ol0 GTPGTP-binding nuclear protein Ran / 0.672
1uad GNPRas-related protein Ral-A / 0.671
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.671
2rgg GNPGTPase HRas / 0.671
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.671
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.671
4d0l GSPRas-related protein Rab-11A / 0.671
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.671
4oi2 ADPProtein clpf-1 / 0.671
4xsg GSPTransforming protein RhoA / 0.671
1n6m ADPProtein claret segregational / 0.670
1s1c GNPTransforming protein RhoA / 0.669
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.669
4idn GNPAtlastin-1 3.6.5 0.669
2zsa ADPPantothenate kinase 2.7.1.33 0.668
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.668
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.668
4hdo GNPRas-related protein Rap-1b / 0.668
4lhv GDPRas-related protein Rab-8A / 0.668
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.667
1z6t ADPApoptotic protease-activating factor 1 / 0.667
2d4h 5GPGuanylate-binding protein 1 / 0.666
3ddc GNPGTPase HRas / 0.666
3lbn GNPGTPase HRas / 0.666
3oiw GNPGTPase HRas / 0.666
1s3g AP5Adenylate kinase / 0.665
3l8y GNPGTPase HRas / 0.665
3rs0 GNPGTPase HRas / 0.665
3thy ADPDNA mismatch repair protein Msh2 / 0.665
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.664
3oiv GNPGTPase HRas / 0.664
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.663
2q3f GNPRas-related GTP-binding protein D / 0.663
3tnf GNPRas-related protein Rab-8A / 0.663
4mkh AP5Adenylate kinase / 0.663
5k5z ANPUncharacterized protein / 0.663
1p9w ANPType II secretion system protein E / 0.662
2zs8 ADPPantothenate kinase 2.7.1.33 0.662
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.662
3zia ATPATP synthase subunit alpha, mitochondrial / 0.662
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.661
3t1t GDPProbable gliding protein mglA / 0.660
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.659
3r9i ADPSeptum site-determining protein MinD / 0.659
4mkf AP5Adenylate kinase / 0.659
3a58 GNPGTP-binding protein RHO1 / 0.658
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.658
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.658
4nh0 ATPESX secretion system protein EccC / 0.658
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.658
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.657
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.657
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.656
1oix GDPRas-related protein Rab-11A / 0.656
2whx ADPGenome polyprotein 3.4.21.91 0.656
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.656
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.656
1xtr GNPGTP-binding protein Rheb / 0.655
4hdq GNPRas-related protein Rap-1b / 0.655
1ank ANPAdenylate kinase / 0.654
1n6l GTPRas-related protein Rab-5A / 0.654
2bme GNPRas-related protein Rab-4A / 0.654
2gbl ATPCircadian clock protein kinase KaiC 2.7.11.1 0.654
3qi2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.654
3tgp GNPGTPase HRas / 0.654
4d9e LCSD-cysteine desulfhydrase / 0.654
1tf7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.653
1u9i ATPCircadian clock protein kinase KaiC 2.7.11.1 0.653
1yu9 GNPRas-related protein Rab-4A / 0.653
3qbt GNPRas-related protein Rab-8A / 0.653
4uj5 GNPRas-related protein Rab-11A / 0.653
2vp2 DGTDeoxynucleoside kinase / 0.652
3k9l GNPGTPase HRas / 0.652
4xvq GNPGTPase HRas / 0.652
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.651
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.651
2cft PLPPyridoxal phosphate phosphatase / 0.650
2zs9 ADPPantothenate kinase 2.7.1.33 0.650