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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
4tl8 AGS Circadian clock protein kinase KaiC 2.7.11.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 1.175
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 1.133
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 1.126
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 1.125
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 1.125
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 1.113
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 1.033
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 1.028
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 1.016
2zts ADPUncharacterized protein / 0.836
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.810
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.803
2gil GTPRas-related protein Rab-6A / 0.802
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.798
1gwn GTPRho-related GTP-binding protein RhoE / 0.795
3zia ATPATP synthase subunit alpha, mitochondrial / 0.794
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.794
4jsy GTPMetallophosphoesterase / 0.793
2r9v ATPATP synthase subunit alpha / 0.792
4dso GSPGTPase KRas / 0.791
1cxz GSPTransforming protein RhoA / 0.790
2ffq GSPRas-related protein Rab-6B / 0.789
4kvg GTPRas-related protein Rap-1A / 0.789
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.788
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.788
4g0n GNPGTPase HRas / 0.788
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.787
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.787
1fnn ADPORC1-type DNA replication protein / 0.784
4qm6 GTPMetallophosphoesterase / 0.784
2c5l GTPGTPase HRas / 0.782
2uyi ADPKinesin-like protein KIF11 / 0.781
2bku GTPGTP-binding nuclear protein Ran / 0.779
2fna ADPUncharacterized protein / 0.779
2gcp GSPRho-related GTP-binding protein RhoC / 0.779
4xsg GSPTransforming protein RhoA / 0.779
1xmv ADPProtein RecA / 0.778
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.777
1t91 GTPRas-related protein Rab-7a / 0.777
4xoi GTPTransforming protein RhoA / 0.777
1m7b GTPRho-related GTP-binding protein RhoE / 0.776
2cl6 CAGGTPase HRas / 0.776
3mjh GTPRas-related protein Rab-5A / 0.776
4asu ADPATP synthase subunit alpha, mitochondrial / 0.776
3tkl GTPRas-related protein Rab-1A / 0.775
1mmg AGSMyosin-2 heavy chain / 0.774
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.774
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.774
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.774
4dvg GSPRho family GTPase / 0.774
1z0d GDPRas-related protein Rab-5C / 0.773
3w3z GTPGTP-binding nuclear protein Ran / 0.773
4cf7 ADPAdenylate kinase / 0.773
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.772
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.772
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.772
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.772
4dxa GSPRas-related protein Rap-1b / 0.772
1tu3 GNPRas-related protein Rab-5A / 0.771
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.771
3dvl ATPCircadian clock protein kinase KaiC 2.7.11.1 0.770
2bc9 GNPGuanylate-binding protein 1 / 0.769
1wdt GTPElongation factor G (EF-G-2) / 0.768
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.768
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.768
3tgp GNPGTPase HRas / 0.768
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.765
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.765
2x2r ADPKinesin-like protein KIF11 / 0.765
4ihq ADPConserved Archaeal protein / 0.765
1kmq GNPTransforming protein RhoA / 0.764
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.763
1l8q ADPChromosomal replication initiator protein DnaA / 0.762
2xae ADPKinesin-like protein KIF11 / 0.762
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.760
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.760
2hld ANPATP synthase subunit alpha, mitochondrial / 0.759
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.759
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.759
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.759
3kko GNPRas-related protein M-Ras / 0.759
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.758
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.758
5dif GNPGTP-binding nuclear protein Ran / 0.758
1ow3 GDPTransforming protein RhoA / 0.757
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.757
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.757
1fmw ATPMyosin-2 heavy chain / 0.756
4k81 GTPGTPase HRas / 0.756
1ake AP5Adenylate kinase / 0.755
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.755
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.755
2c96 ATPPsp operon transcriptional activator / 0.755
3cob ADPKinesin heavy chain-like protein / 0.755
3kz1 GSPTransforming protein RhoA / 0.755
2y65 ADPKinesin heavy chain / 0.754
3law GNPRas-related protein Rab-7a / 0.754
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.754
5dha GNPGTP-binding nuclear protein Ran / 0.754
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.753
1yzq GNPRas-related protein Rab-6A / 0.753
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.753
3ea5 GDPGTP-binding nuclear protein Ran / 0.753
2pg2 ADPKinesin-like protein KIF11 / 0.752
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.752
4c30 ANPDNA helicase / 0.752
4v02 ATPSite-determining protein / 0.752
5dac AGSUncharacterized protein / 0.752
1wbb ADPDNA mismatch repair protein MutS / 0.751
2j5x GSPADP-ribosylation factor 6 / 0.751
2x7e ADPKinesin-like protein KIF11 / 0.751
1wa5 GTPGTP-binding nuclear protein Ran / 0.750
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.750
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.750
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.749
2zfi ADPKinesin-like protein KIF1A / 0.749
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.749
4js0 GNPCell division control protein 42 homolog / 0.749
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.749
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.748
4d81 ADPAAA ATPase, central domain protein / 0.748
1a2b GSPTransforming protein RhoA / 0.746
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.746
1svm ATPLarge T antigen 3.6.4 0.746
1zc3 GNPRas-related protein Ral-A / 0.746
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.746
3l9h ADPKinesin-like protein KIF11 / 0.746
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.746
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.745
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.745
4dls GNPGTPase HRas / 0.745
4q03 GDPGTPase KRas / 0.745
3k9l GNPGTPase HRas / 0.744
4ldj GDPGTPase KRas / 0.744
4lhw GNPRas-related protein Rab-8A / 0.744
4nh0 ATPESX secretion system protein EccC / 0.744
1g17 GNPRas-related protein SEC4 / 0.743
1sdm ADPKinesin heavy chain-like protein / 0.743
1w5t ANPORC1-type DNA replication protein 2 / 0.743
3qbt GNPRas-related protein Rab-8A / 0.743
4obe GDPGTPase KRas / 0.743
4y0v GDPADP-ribosylation factor 1, putative / 0.743
4ylg GDPADP-ribosylation factor 1, putative / 0.743
5ftc ADPTPR domain protein / 0.743
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.742
1w5t ADPORC1-type DNA replication protein 2 / 0.742
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.742
3tso GNPRas-related protein Rab-25 / 0.742
1z0f GDPRas-related protein Rab-14 / 0.741
1zc4 GNPRas-related protein Ral-A / 0.741
2dr3 ADPUPF0273 protein PH0284 / 0.741
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.741
4jlo ADPAdenylate kinase / 0.741
4qos ADPPsp operon transcriptional activator / 0.741
1b7t ADPMyosin heavy chain, striated muscle / 0.740
3d8b ADPFidgetin-like protein 1 3.6.4 0.740
3wyf GTPGTP-binding nuclear protein / 0.740
5di3 GNPADP-ribosylation factor-like protein 3 / 0.739
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.738
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.738
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.738
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.737
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.737
4yqf GDPSeptin-9 / 0.737
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.736
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.736
5c46 GSPRas-related protein Rab-11A / 0.736
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.735
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.735
4dzz ADPPlasmid partitioning protein ParF / 0.735
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.734
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.734
1svl ADPLarge T antigen 3.6.4 0.734
4dsu GDPGTPase KRas / 0.734
2j7p GNPSignal recognition particle protein / 0.733
2j7p GNPSignal recognition particle receptor FtsY / 0.733
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.733
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.732
3lbh GNPGTPase HRas / 0.731
5l3s GNPSignal recognition particle receptor FtsY / 0.731
2gm1 ADPKinesin-like protein KIF11 / 0.730
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.730
2iut AGSDNA translocase FtsK / 0.729
4qxa GTPRas-related protein Rab-9A / 0.729
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.728
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.728
1uad GNPRas-related protein Ral-A / 0.727
4oi2 ADPProtein clpf-1 / 0.727
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.726
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.726
5da9 AGSUncharacterized protein / 0.726
1yrs ADPKinesin-like protein KIF11 / 0.725
4zca ADPKinesin-like protein KIF11 / 0.725
3t1t GDPProbable gliding protein mglA / 0.724
4l9s GDPGTPase HRas / 0.724
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.723
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.723
2ql6 ADPNicotinamide riboside kinase 1 / 0.723
3bc1 GNPRas-related protein Rab-27A / 0.723
3e5h GNPRas-related protein Rab-28 / 0.723
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.722
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.721
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.721
2fg5 GNPRas-related protein Rab-31 / 0.721
2osb AP5Adenylate kinase / 0.721
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.721
4luc GDPGTPase KRas / 0.721
1k5d GNPGTP-binding nuclear protein Ran / 0.720
3eg5 GNPCell division control protein 42 homolog / 0.720
3m0e ATPTranscriptional regulator (NtrC family) / 0.720
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.720
4d0l GSPRas-related protein Rab-11A / 0.719
4l8g GDPGTPase KRas / 0.719
4w5j AP5Adenylate kinase / 0.719
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.718
4mkg AP5Adenylate kinase / 0.718
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.716
1p3j AP5Adenylate kinase / 0.715
4b7b ADPKinesin-like protein KIF11 / 0.714
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.713
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.712
2eck ADPAdenylate kinase / 0.712
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.712
2fl2 ADPKinesin-like protein KIF11 / 0.710
4a28 ADPKinesin-like protein KIF11 / 0.710
1v8k ANPKinesin-like protein KIF2C / 0.709
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.709
4hse ADPChaperone protein ClpB / 0.709
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.708
2l0x GDPGTP-binding protein Rheb / 0.707
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.705
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.705
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.705
2gbl ATPCircadian clock protein kinase KaiC 2.7.11.1 0.705
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.705
4jjz ADPFormate--tetrahydrofolate ligase / 0.705
1z0a GDPRas-related protein Rab-2A / 0.704
4qnr ATPPsp operon transcriptional activator / 0.704
1rj9 GCPSignal recognition particle receptor FtsY / 0.703
4ohx ADPProtein clpf-1 / 0.703
5aun ADPIron-sulfur cluster carrier protein / 0.703
1okk GCPSignal recognition particle protein / 0.702
1okk GCPSignal recognition particle receptor FtsY / 0.702
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.702
3fkq ATPNtrC-like two-domain protein / 0.701
1ii6 ADPKinesin-like protein KIF11 / 0.700
4epx GDPGTPase KRas / 0.700
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.698
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.698
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.697
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.697
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.697
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.697
1jx2 ADPMyosin-2 heavy chain / 0.695
4itr GDPCell division control protein 42 homolog / 0.695
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.694
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.694
1ny5 ADPTranscriptional regulator (NtrC family) / 0.692
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.692
4iei ADPGene 2 protein / 0.692
2c9c ATPPsp operon transcriptional activator / 0.691
1sxj AGSReplication factor C subunit 1 / 0.690
3dkv AP5Adenylate kinase / 0.690
3pcr GTPADP-ribosylation factor 6 / 0.690
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.690
4uj5 GNPRas-related protein Rab-11A / 0.690
3k0f ATPCircadian clock protein kinase KaiC 2.7.11.1 0.689
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.688
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
1rrg GDPADP-ribosylation factor 1 / 0.688
2g1q ADPKinesin-like protein KIF11 / 0.687
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.687
2cls GTPRho-related GTP-binding protein Rho6 / 0.686
3l1c ADPProtein claret segregational / 0.686
4nu0 AP5Adenylate kinase / 0.686
4pjk ADPMyosin-2 heavy chain / 0.686
1esn ANPPantothenate kinase 2.7.1.33 0.685
1tf7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.685
1u9i ATPCircadian clock protein kinase KaiC 2.7.11.1 0.685
2rgx AP5Adenylate kinase / 0.684
5hpy GDPTransforming protein RhoA / 0.684
3k1j ADPATP-dependent protease Lon / 0.683
4pfp ADPUnconventional myosin-VI / 0.683
3k3b ADPKinesin-like protein KIF11 / 0.682
3x1w GDPRas-related protein Rap-1b / 0.680
4o2l GTPGTP-binding protein Rheb / 0.680
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.679
3nbx ADPATPase RavA 3.6.3 0.678
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.678
1mab ATPATP synthase subunit alpha, mitochondrial / 0.677
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.676
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.674
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.673
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.670
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.670
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.669
4ohv ANPProtein clpf-1 / 0.669
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.668
2pz8 APCNH(3)-dependent NAD(+) synthetase / 0.668
2vf7 ADPUvrABC system protein A / 0.668
5ftf ADPTPR domain protein / 0.667
4o0m ATPCircadian clock protein kinase KaiC 2.7.11.1 0.666
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.665
1p9w ANPType II secretion system protein E / 0.664
2jcs TTPDeoxynucleoside kinase / 0.663
2zro ADPProtein RecA / 0.663
3hqd ANPKinesin-like protein KIF11 / 0.663
4o25 GTPGTP-binding protein Rheb / 0.662
3a6p GTPGTP-binding nuclear protein Ran / 0.661
3q9l ATPSeptum site-determining protein MinD / 0.661
4lpk GDPGTPase KRas / 0.661
3thy ADPDNA mismatch repair protein Msh2 / 0.660
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.659
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.659
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.659
2eu8 AP5Adenylate kinase / 0.658
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.658
3s1a ATPCircadian clock protein kinase KaiC 2.7.11.1 0.658
4o3m ADPBloom syndrome protein 3.6.4.12 0.658
2ce2 GDPGTPase HRas / 0.657
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.656
3jzm ATPCircadian clock protein kinase KaiC 2.7.11.1 0.656
4qbg AP5Adenylate kinase / 0.656
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.654
4mit GTPRho-related protein racC / 0.652
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.650
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.650
3pff ADPATP-citrate synthase 2.3.3.8 0.650