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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
4tla ADP 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
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 1.210
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 1.067
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 1.055
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 1.035
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 1.032
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 1.016
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 1.012
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 1.002
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.961
2zts ADPUncharacterized protein / 0.927
1xmv ADPProtein RecA / 0.826
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.815
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.815
4ldj GDPGTPase KRas / 0.813
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.812
4pjk ADPMyosin-2 heavy chain / 0.812
2xae ADPKinesin-like protein KIF11 / 0.798
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.793
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.793
5cyo GDPSeptin-9 / 0.792
2y65 ADPKinesin heavy chain / 0.791
1sdm ADPKinesin heavy chain-like protein / 0.787
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.786
2dr3 ADPUPF0273 protein PH0284 / 0.785
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.785
4obe GDPGTPase KRas / 0.782
2qen ADPWalker-Type ATPase / 0.781
4z54 GDPNeuronal-specific septin-3 / 0.781
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.780
4cf7 ADPAdenylate kinase / 0.776
1wbb ADPDNA mismatch repair protein MutS / 0.775
4dzz ADPPlasmid partitioning protein ParF / 0.773
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.772
4dso GSPGTPase KRas / 0.772
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.771
3wyf GTPGTP-binding nuclear protein / 0.770
1ow3 GDPTransforming protein RhoA / 0.769
1z0d GDPRas-related protein Rab-5C / 0.769
4qxa GTPRas-related protein Rab-9A / 0.769
4luc GDPGTPase KRas / 0.765
4mkf AP5Adenylate kinase / 0.764
1sq5 ADPPantothenate kinase 2.7.1.33 0.762
3k0f ATPCircadian clock protein kinase KaiC 2.7.11.1 0.762
4ihq ADPConserved Archaeal protein / 0.762
1mma ADPMyosin-2 heavy chain / 0.760
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.760
3dvl ATPCircadian clock protein kinase KaiC 2.7.11.1 0.760
4xsg GSPTransforming protein RhoA / 0.760
4zca ADPKinesin-like protein KIF11 / 0.760
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.759
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.757
3zia ATPATP synthase subunit alpha, mitochondrial / 0.757
4hse ADPChaperone protein ClpB / 0.757
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.755
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.755
1d5c GDPGTPase (Rab6) / 0.754
4y0v GDPADP-ribosylation factor 1, putative / 0.754
4ylg GDPADP-ribosylation factor 1, putative / 0.754
1f5n GNPGuanylate-binding protein 1 / 0.752
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.752
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.752
5dac AGSUncharacterized protein / 0.752
1ake AP5Adenylate kinase / 0.751
3law GNPRas-related protein Rab-7a / 0.750
3rab GNPRas-related protein Rab-3A / 0.750
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.750
4asu ADPATP synthase subunit alpha, mitochondrial / 0.744
4a1z ADPKinesin-like protein KIF11 / 0.743
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.742
1svl ADPLarge T antigen 3.6.4 0.742
2rgx AP5Adenylate kinase / 0.741
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.740
2gm1 ADPKinesin-like protein KIF11 / 0.740
3myk ANPMyosin-2 heavy chain / 0.740
4iok ADPFormate--tetrahydrofolate ligase / 0.740
1oix GDPRas-related protein Rab-11A / 0.737
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.737
2fl2 ADPKinesin-like protein KIF11 / 0.737
2gil GTPRas-related protein Rab-6A / 0.737
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.737
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.736
3pcr GTPADP-ribosylation factor 6 / 0.736
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.735
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.735
4pjj ADPUnconventional myosin-VI / 0.735
1z0a GDPRas-related protein Rab-2A / 0.734
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.734
3ftq GNPSeptin-2 / 0.734
1jx2 ADPMyosin-2 heavy chain / 0.732
3mjh GTPRas-related protein Rab-5A / 0.732
5dha GNPGTP-binding nuclear protein Ran / 0.732
1w5t ANPORC1-type DNA replication protein 2 / 0.731
4xvq GNPGTPase HRas / 0.731
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.728
2cls GTPRho-related GTP-binding protein Rho6 / 0.727
5l3s GNPSignal recognition particle receptor FtsY / 0.727
5dif GNPGTP-binding nuclear protein Ran / 0.726
5ftc ADPTPR domain protein / 0.725
2zrj AGSProtein RecA / 0.724
4yqf GDPSeptin-9 / 0.724
1ky2 GNPGTP-binding protein YPT7 / 0.722
2bc9 GNPGuanylate-binding protein 1 / 0.721
1a2b GSPTransforming protein RhoA / 0.720
1am4 GNPCell division control protein 42 homolog / 0.720
1wa5 GTPGTP-binding nuclear protein Ran / 0.719
3tjz GNPADP-ribosylation factor 1 / 0.719
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.718
4a28 ADPKinesin-like protein KIF11 / 0.718
1mmg AGSMyosin-2 heavy chain / 0.717
5di3 GNPADP-ribosylation factor-like protein 3 / 0.717
2fna ADPUncharacterized protein / 0.716
2q3f GNPRas-related GTP-binding protein D / 0.716
4ql3 GDPGTPase KRas / 0.716
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.715
1kmq GNPTransforming protein RhoA / 0.714
1z6t ADPApoptotic protease-activating factor 1 / 0.714
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.713
1z2c GNPRho-related GTP-binding protein RhoC / 0.712
2dpx GDPGTP-binding protein RAD / 0.712
4uj3 GNPRas-related protein Rab-11A / 0.712
2j7p GNPSignal recognition particle protein / 0.711
2j7p GNPSignal recognition particle receptor FtsY / 0.711
4dxa GSPRas-related protein Rap-1b / 0.711
1zc3 GNPRas-related protein Ral-A / 0.710
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
4epx GDPGTPase KRas / 0.710
4ol0 GTPGTP-binding nuclear protein Ran / 0.710
4lrw GDPGTPase KRas / 0.709
1t91 GTPRas-related protein Rab-7a / 0.708
5c46 GSPRas-related protein Rab-11A / 0.708
2hld ANPATP synthase subunit alpha, mitochondrial / 0.707
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.707
4pfp ADPUnconventional myosin-VI / 0.707
2bku GTPGTP-binding nuclear protein Ran / 0.706
2osb AP5Adenylate kinase / 0.706
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.705
1ny5 ADPTranscriptional regulator (NtrC family) / 0.705
1yra GDPGPN-loop GTPase PAB0955 / 0.705
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.705
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.705
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.705
3ddc GNPGTPase HRas / 0.704
3s1a ATPCircadian clock protein kinase KaiC 2.7.11.1 0.704
4g0n GNPGTPase HRas / 0.704
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.703
1fnn ADPORC1-type DNA replication protein / 0.702
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.702
1g17 GNPRas-related protein SEC4 / 0.701
4jjz ADPFormate--tetrahydrofolate ligase / 0.701
1okk GCPSignal recognition particle protein / 0.700
1okk GCPSignal recognition particle receptor FtsY / 0.700
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.700
2pg2 ADPKinesin-like protein KIF11 / 0.700
3kud GDPGTPase HRas / 0.700
4a51 ADPKinesin-like protein KIF11 / 0.700
4ohx ADPProtein clpf-1 / 0.700
1ank ANPAdenylate kinase / 0.699
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.699
4dsu GDPGTPase KRas / 0.699
4js0 GNPCell division control protein 42 homolog / 0.699
2uyi ADPKinesin-like protein KIF11 / 0.698
3oiv GNPGTPase HRas / 0.698
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.698
4ap0 ADPKinesin-like protein KIF11 / 0.698
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.697
1n6l GTPRas-related protein Rab-5A / 0.697
2x2r ADPKinesin-like protein KIF11 / 0.697
1nly AGSCag alpha / 0.696
2whx ADPGenome polyprotein 3.4.21.91 0.696
1tf7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.695
1u9i ATPCircadian clock protein kinase KaiC 2.7.11.1 0.695
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.695
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
3kuc GDPRas-related protein Rap-1A / 0.695
3tso GNPRas-related protein Rab-25 / 0.695
4ys0 ADPProtein translocase subunit SecA / 0.695
2eck ADPAdenylate kinase / 0.694
2x7e ADPKinesin-like protein KIF11 / 0.694
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.693
2ce2 GDPGTPase HRas / 0.692
4cym GCPRas-related protein Rab-32 / 0.692
5bn3 ADPV-type ATP synthase alpha chain / 0.692
5bn3 ADPNEQ263 / 0.692
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.691
2uz3 TTPThymidine kinase / 0.691
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.690
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
1sxj ADPReplication factor C subunit 5 / 0.690
2fe4 GDPRas-related protein Rab-6B / 0.690
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.690
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.690
2cl6 CAGGTPase HRas / 0.689
4c30 ANPDNA helicase / 0.689
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.688
1yu9 GNPRas-related protein Rab-4A / 0.688
2rge GNPGTPase HRas / 0.688
3cob ADPKinesin heavy chain-like protein / 0.688
3l8y GNPGTPase HRas / 0.688
3lbh GNPGTPase HRas / 0.688
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.688
4dls GNPGTPase HRas / 0.688
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.688
1fmw ATPMyosin-2 heavy chain / 0.687
1xms ANPProtein RecA / 0.686
3lbi GNPGTPase HRas / 0.686
1gwn GTPRho-related GTP-binding protein RhoE / 0.685
2gbl ATPCircadian clock protein kinase KaiC 2.7.11.1 0.685
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.685
4l9s GDPGTPase HRas / 0.684
1ii6 ADPKinesin-like protein KIF11 / 0.683
2bme GNPRas-related protein Rab-4A / 0.683
3qbv GDPCell division control protein 42 homolog / 0.683
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.683
3x1w GDPRas-related protein Rap-1b / 0.683
5aun ADPIron-sulfur cluster carrier protein / 0.683
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.682
3eg5 GNPCell division control protein 42 homolog / 0.682
3kkq GDPRas-related protein M-Ras / 0.682
4q02 GDPGTPase KRas / 0.682
4tq9 GDPGTPase KRas / 0.682
2o8b ADPDNA mismatch repair protein Msh2 / 0.681
3k3b ADPKinesin-like protein KIF11 / 0.681
3thy ADPDNA mismatch repair protein Msh2 / 0.681
4lv6 GDPGTPase KRas / 0.681
3e5h GNPRas-related protein Rab-28 / 0.680
4hut ATPCob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 0.680
4o3m ADPBloom syndrome protein 3.6.4.12 0.680
4wa7 GDPGTPase KRas / 0.680
5k5z ANPUncharacterized protein / 0.680
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.679
3cph GDPRas-related protein SEC4 / 0.679
3pit GNPRas-related protein M-Ras / 0.679
4l8g GDPGTPase KRas / 0.679
1v8k ANPKinesin-like protein KIF2C / 0.678
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.678
3bc1 GNPRas-related protein Rab-27A / 0.678
3jzm ATPCircadian clock protein kinase KaiC 2.7.11.1 0.678
3q5d GDPAtlastin-1 3.6.5 0.678
4kvg GTPRas-related protein Rap-1A / 0.678
1z2a GDPRas-related protein Rab-23 / 0.677
1zbd GTPRas-related protein Rab-3A / 0.677
2ad5 ADPCTP synthase / 0.677
4epw GDPGTPase KRas / 0.677
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
2rgg GNPGTPase HRas / 0.676
3c41 ANPAmino acid ABC transporter / 0.676
1l8q ADPChromosomal replication initiator protein DnaA / 0.675
1zc4 GNPRas-related protein Ral-A / 0.675
3sop GDPNeuronal-specific septin-3 / 0.675
3tgp GNPGTPase HRas / 0.675
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.673
2iut AGSDNA translocase FtsK / 0.672
3i3s GNPGTPase HRas / 0.672
3k8y GNPGTPase HRas / 0.672
3k9l GNPGTPase HRas / 0.672
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.672
4lhw GNPRas-related protein Rab-8A / 0.672
4xoi GTPTransforming protein RhoA / 0.672
4fvr ATPTyrosine-protein kinase JAK2 / 0.671
1uad GNPRas-related protein Ral-A / 0.670
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.670
3x1z GNPRas-related protein Rap-1b / 0.670
1w5t ADPORC1-type DNA replication protein 2 / 0.668
2vf7 ADPUvrABC system protein A / 0.668
3rs5 GNPGTPase HRas / 0.668
4nyj GNPGTPase HRas / 0.668
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.667
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
1tu3 GNPRas-related protein Rab-5A / 0.667
3qbt GNPRas-related protein Rab-8A / 0.667
3rs4 GNPGTPase HRas / 0.667
4dlw GNPGTPase HRas / 0.667
2rgc GNPGTPase HRas / 0.666
3rs7 GNPGTPase HRas / 0.666
4pk4 ADPUnconventional myosin-VI / 0.666
5cyp GSPSeptin-9 / 0.666
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.665
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.664
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
2zet GTPRas-related protein Rab-27B / 0.664
2zro ADPProtein RecA / 0.662
3tkl GTPRas-related protein Rab-1A / 0.662
3l9h ADPKinesin-like protein KIF11 / 0.661
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.661
4uj5 GNPRas-related protein Rab-11A / 0.661
3k1j ADPATP-dependent protease Lon / 0.660
3oiu GNPGTPase HRas / 0.659
3v4f GNPGTPase HRas / 0.659
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.659
4b7b ADPKinesin-like protein KIF11 / 0.659
4dlv GNPGTPase HRas / 0.659
4lpk GDPGTPase KRas / 0.659
4uxj TTPThymidine kinase / 0.659
5b2z GNPGTPase HRas / 0.659
1svw GTPProbable GTP-binding protein EngB / 0.658
1xp8 AGSProtein RecA / 0.658
2zsa ADPPantothenate kinase 2.7.1.33 0.658
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.658
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.658
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.657
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.657
5jlj GNPGTP-binding nuclear protein Ran / 0.657
1rrg GDPADP-ribosylation factor 1 / 0.656
3oes GNPGTPase RhebL1 / 0.656
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.655
3rs0 GNPGTPase HRas / 0.655
4nh0 ATPESX secretion system protein EccC / 0.655
4rkf GNPRas-related protein Rab-3 / 0.655
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.654
2rgb GNPGTPase HRas / 0.654
4dlt GNPGTPase HRas / 0.654
4dsn GCPGTPase KRas / 0.654
4hdo GNPRas-related protein Rap-1b / 0.654
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.653
3lbn GNPGTPase HRas / 0.653
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.653
3rsl GNPGTPase HRas / 0.653
4dlx GNPGTPase HRas / 0.653
4l9w GNPGTPase HRas / 0.653
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.653
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.652
1n6m ADPProtein claret segregational / 0.651
2j5x GSPADP-ribosylation factor 6 / 0.651
2ncd ADPProtein claret segregational / 0.651
4gp6 ADPMetallophosphoesterase / 0.651
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.650
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
1s1c GNPTransforming protein RhoA / 0.650
2fg5 GNPRas-related protein Rab-31 / 0.650
4itr GDPCell division control protein 42 homolog / 0.650
4mit GTPRho-related protein racC / 0.650
4nyi GNPGTPase HRas / 0.650