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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
3l1c ADP Protein claret segregational

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3l1c ADPProtein claret segregational / 0.889
4b7b ADPKinesin-like protein KIF11 / 0.790
2zfi ADPKinesin-like protein KIF1A / 0.788
1sdm ADPKinesin heavy chain-like protein / 0.779
2xae ADPKinesin-like protein KIF11 / 0.777
2q2z ADPKinesin-like protein KIF11 / 0.776
2y65 ADPKinesin heavy chain / 0.773
2fl2 ADPKinesin-like protein KIF11 / 0.769
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.767
3l9h ADPKinesin-like protein KIF11 / 0.766
1yrs ADPKinesin-like protein KIF11 / 0.764
4hse ADPChaperone protein ClpB / 0.764
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.763
2x2r ADPKinesin-like protein KIF11 / 0.760
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.760
4a28 ADPKinesin-like protein KIF11 / 0.758
4wa7 GDPGTPase KRas / 0.758
3tlx ADPAdenylate kinase 2 / 0.755
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.753
2gm1 ADPKinesin-like protein KIF11 / 0.750
2uyi ADPKinesin-like protein KIF11 / 0.749
3cob ADPKinesin heavy chain-like protein / 0.748
2pg2 ADPKinesin-like protein KIF11 / 0.746
2zts ADPUncharacterized protein / 0.746
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.746
4zca ADPKinesin-like protein KIF11 / 0.745
1jsz NDMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 2.1.1.57 0.744
1xmv ADPProtein RecA / 0.744
2whx ADPGenome polyprotein 3.4.21.91 0.744
4l8g GDPGTPase KRas / 0.744
3d8b ADPFidgetin-like protein 1 3.6.4 0.743
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.742
3kkq GDPRas-related protein M-Ras / 0.742
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.742
1ii6 ADPKinesin-like protein KIF11 / 0.741
1jx2 ADPMyosin-2 heavy chain / 0.741
1sq5 ADPPantothenate kinase 2.7.1.33 0.741
1z0a GDPRas-related protein Rab-2A / 0.741
4epw GDPGTPase KRas / 0.741
4l9s GDPGTPase HRas / 0.740
4ldj GDPGTPase KRas / 0.740
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.739
3kud GDPGTPase HRas / 0.739
4lv6 GDPGTPase KRas / 0.739
4pfp ADPUnconventional myosin-VI / 0.739
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.738
1z2a GDPRas-related protein Rab-23 / 0.738
4ql3 GDPGTPase KRas / 0.738
4tq9 GDPGTPase KRas / 0.738
1zbd GTPRas-related protein Rab-3A / 0.737
3x1w GDPRas-related protein Rap-1b / 0.737
4dsu GDPGTPase KRas / 0.737
4dzz ADPPlasmid partitioning protein ParF / 0.737
4epx GDPGTPase KRas / 0.737
4pjj ADPUnconventional myosin-VI / 0.737
4q02 GDPGTPase KRas / 0.737
1mma ADPMyosin-2 heavy chain / 0.736
1d5c GDPGTPase (Rab6) / 0.735
2fna ADPUncharacterized protein / 0.735
4lhv GDPRas-related protein Rab-8A / 0.734
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.732
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.732
4obe GDPGTPase KRas / 0.732
4z54 GDPNeuronal-specific septin-3 / 0.732
4luc GDPGTPase KRas / 0.731
5bn3 ADPV-type ATP synthase alpha chain / 0.731
5bn3 ADPNEQ263 / 0.731
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.730
4cf7 ADPAdenylate kinase / 0.729
4jlo ADPAdenylate kinase / 0.729
4pjk ADPMyosin-2 heavy chain / 0.729
3q5d GDPAtlastin-1 3.6.5 0.728
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.728
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.726
4hi0 GDPUrease accessory protein UreG / 0.726
5aun ADPIron-sulfur cluster carrier protein / 0.726
5ftc ADPTPR domain protein / 0.726
1oix GDPRas-related protein Rab-11A / 0.725
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.725
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.725
2vos ADPFolylpolyglutamate synthase / 0.725
4a51 ADPKinesin-like protein KIF11 / 0.725
1fnn ADPORC1-type DNA replication protein / 0.724
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.724
1z0d GDPRas-related protein Rab-5C / 0.723
3ref GDPRho family GTPase / 0.723
3tqc ADPPantothenate kinase / 0.723
4jl5 ADPAdenylate kinase / 0.723
4q03 GDPGTPase KRas / 0.723
1x1r GDPRas-related protein M-Ras / 0.722
4o2r GDPGTP-binding protein Rheb / 0.722
1b7t ADPMyosin heavy chain, striated muscle / 0.720
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.720
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.720
1ow3 GDPTransforming protein RhoA / 0.720
3cph GDPRas-related protein SEC4 / 0.720
4ike ADPAdenylate kinase / 0.720
4jld ADPAdenylate kinase / 0.720
1w5s ADPORC1-type DNA replication protein 2 / 0.719
4lrw GDPGTPase KRas / 0.719
1ake AP5Adenylate kinase / 0.718
1mmg AGSMyosin-2 heavy chain / 0.718
2g1q ADPKinesin-like protein KIF11 / 0.718
4a1z ADPKinesin-like protein KIF11 / 0.718
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.717
4pk4 ADPUnconventional myosin-VI / 0.717
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.716
1yra GDPGPN-loop GTPase PAB0955 / 0.716
3m0e ATPTranscriptional regulator (NtrC family) / 0.716
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.716
1wbb ADPDNA mismatch repair protein MutS / 0.715
2eck ADPAdenylate kinase / 0.715
2zro ADPProtein RecA / 0.715
2dft ADPShikimate kinase 2.7.1.71 0.714
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.713
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.713
1rrg GDPADP-ribosylation factor 1 / 0.713
4asu ADPATP synthase subunit alpha, mitochondrial / 0.713
1w5t ADPORC1-type DNA replication protein 2 / 0.712
3mjh GTPRas-related protein Rab-5A / 0.712
4ihq ADPConserved Archaeal protein / 0.711
4mkf AP5Adenylate kinase / 0.711
1l8q ADPChromosomal replication initiator protein DnaA / 0.710
2j5x GSPADP-ribosylation factor 6 / 0.710
4qbg AP5Adenylate kinase / 0.710
4ys0 ADPProtein translocase subunit SecA / 0.710
1z0f GDPRas-related protein Rab-14 / 0.709
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.709
4jl6 ADPAdenylate kinase / 0.709
1g16 GDPRas-related protein SEC4 / 0.708
4jky ADPAdenylate kinase / 0.708
2x7e ADPKinesin-like protein KIF11 / 0.707
3ieu GDPGTPase Era / 0.707
4o3m ADPBloom syndrome protein 3.6.4.12 0.707
4qos ADPPsp operon transcriptional activator / 0.707
1nly AGSCag alpha / 0.706
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.706
2vor ACPFolylpolyglutamate synthase / 0.705
4lpk GDPGTPase KRas / 0.705
5cyo GDPSeptin-9 / 0.705
4gp6 ADPMetallophosphoesterase / 0.704
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.703
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.702
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.702
1svl ADPLarge T antigen 3.6.4 0.701
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.701
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.701
2ce2 GDPGTPase HRas / 0.700
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.700
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.700
3ea5 GDPGTP-binding nuclear protein Ran / 0.700
4qm6 GTPMetallophosphoesterase / 0.700
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.700
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.699
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.699
1ny5 ADPTranscriptional regulator (NtrC family) / 0.698
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.698
2dr3 ADPUPF0273 protein PH0284 / 0.698
3tgp GNPGTPase HRas / 0.698
4xvr GNPGTPase HRas / 0.698
2c96 ATPPsp operon transcriptional activator / 0.697
3qbv GDPCell division control protein 42 homolog / 0.697
4xvq GNPGTPase HRas / 0.697
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.696
4ap0 ADPKinesin-like protein KIF11 / 0.696
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.695
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.695
2r9v ATPATP synthase subunit alpha / 0.695
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.695
3vhx GTPADP-ribosylation factor 6 / 0.695
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.694
3k1j ADPATP-dependent protease Lon / 0.693
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.693
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.692
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.691
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.691
1z6t ADPApoptotic protease-activating factor 1 / 0.690
2fe4 GDPRas-related protein Rab-6B / 0.690
1m7b GTPRho-related GTP-binding protein RhoE / 0.689
1n6m ADPProtein claret segregational / 0.689
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.689
3zia ATPATP synthase subunit alpha, mitochondrial / 0.689
4itr GDPCell division control protein 42 homolog / 0.689
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.688
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.688
3oee ANPATP synthase subunit alpha, mitochondrial / 0.688
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.688
4xsg GSPTransforming protein RhoA / 0.688
3kuc GDPRas-related protein Rap-1A / 0.687
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.687
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.687
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.687
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.686
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.686
2l0x GDPGTP-binding protein Rheb / 0.686
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.686
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.686
1sxj ADPReplication factor C subunit 5 / 0.685
4mit GTPRho-related protein racC / 0.685
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.684
1m67 BOAGlycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal 1.1.1.8 0.684
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.684
1uad GNPRas-related protein Ral-A / 0.684
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.684
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.684
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.683
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.683
3k9l GNPGTPase HRas / 0.683
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.683
3c41 ANPAmino acid ABC transporter / 0.682
3myk ANPMyosin-2 heavy chain / 0.682
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.682
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.681
1lfd GNPGTPase HRas / 0.681
2rgg GNPGTPase HRas / 0.681
4o2l GTPGTP-binding protein Rheb / 0.681
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.680
1p9w ANPType II secretion system protein E / 0.680
1xtr GNPGTP-binding protein Rheb / 0.680
4dls GNPGTPase HRas / 0.680
1g17 GNPRas-related protein SEC4 / 0.679
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.679
4lhw GNPRas-related protein Rab-8A / 0.679
4rkf GNPRas-related protein Rab-3 / 0.678
1zio AP5Adenylate kinase / 0.677
5fm6 ADPRuvB-like helicase / 0.677
1n6l GTPRas-related protein Rab-5A / 0.676
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.676
3oes GNPGTPase RhebL1 / 0.676
3thy ADPDNA mismatch repair protein Msh2 / 0.676
1esn ANPPantothenate kinase 2.7.1.33 0.675
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.675
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.675
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.675
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.674
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.674
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.674
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.674
2c9c ATPPsp operon transcriptional activator / 0.673
2q2y ADPKinesin-like protein KIF11 / 0.673
4cym GCPRas-related protein Rab-32 / 0.673
4dxa GSPRas-related protein Rap-1b / 0.673
2uz3 TTPThymidine kinase / 0.672
4hdq GNPRas-related protein Rap-1b / 0.672
4ncl GDPEukaryotic translation initiation factor 5B / 0.672
4nh0 ATPESX secretion system protein EccC / 0.672
4xoi GTPTransforming protein RhoA / 0.672
2q3f GNPRas-related GTP-binding protein D / 0.670
4qnr ATPPsp operon transcriptional activator / 0.670
1ky2 GNPGTP-binding protein YPT7 / 0.669
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.669
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.668
1w5t ANPORC1-type DNA replication protein 2 / 0.668
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.668
4goj GNPADP-ribosylation factor-like protein 3 / 0.668
5di3 GNPADP-ribosylation factor-like protein 3 / 0.668
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.667
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.667
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.667
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.667
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.666
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.666
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.666
2zr9 DTPProtein RecA / 0.665
4qxa GTPRas-related protein Rab-9A / 0.665
2dpx GDPGTP-binding protein RAD / 0.664
3tso GNPRas-related protein Rab-25 / 0.664
4yqf GDPSeptin-9 / 0.664
5hpy GDPTransforming protein RhoA / 0.664
1v8k ANPKinesin-like protein KIF2C / 0.663
1z2c GNPRho-related GTP-binding protein RhoC / 0.663
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.663
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.663
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.663
3t1t GDPProbable gliding protein mglA / 0.663
4rzu ADPProbable thymidylate kinase 2.7.4.9 0.663
4xvu ATPATPase GET3 / 0.663
5k5z ANPUncharacterized protein / 0.663
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.662
1mab ATPATP synthase subunit alpha, mitochondrial / 0.662
1tu3 GNPRas-related protein Rab-5A / 0.662
1yu9 GNPRas-related protein Rab-4A / 0.662
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.662
1g6o ADPCag alpha / 0.661
3hqd ANPKinesin-like protein KIF11 / 0.661
1i7c MGBS-adenosylmethionine decarboxylase proenzyme 4.1.1.50 0.660
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
3tjz GNPADP-ribosylation factor 1 / 0.660
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.660
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.659
3qi2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.658
4iok ADPFormate--tetrahydrofolate ligase / 0.657
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.656
2e8u IPEGeranylgeranyl pyrophosphate synthase / 0.656
3bc1 GNPRas-related protein Rab-27A / 0.656
3kko GNPRas-related protein M-Ras / 0.656
3law GNPRas-related protein Rab-7a / 0.656
3nbx ADPATPase RavA 3.6.3 0.656
4beb ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.656
1xms ANPProtein RecA / 0.655
3a58 GNPGTP-binding protein RHO1 / 0.655
4yaw 2AMNADPH--cytochrome P450 reductase / 0.655
2o8b ADPDNA mismatch repair protein Msh2 / 0.654
2qen ADPWalker-Type ATPase / 0.654
3pcr GTPADP-ribosylation factor 6 / 0.654
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.653
3r9x GNPGTPase Era / 0.653
4uj3 GNPRas-related protein Rab-11A / 0.653
4yal 2AMNADPH--cytochrome P450 reductase / 0.653
1am4 GNPCell division control protein 42 homolog / 0.652
1rj9 GCPSignal recognition particle receptor FtsY / 0.652
3qbt GNPRas-related protein Rab-8A / 0.652
4ovi N01Phenylacetone monooxygenase 1.14.13.92 0.652
2xsz ATPRuvB-like 2 3.6.4.12 0.651
4idn GNPAtlastin-1 3.6.5 0.651
1oyy AGSATP-dependent DNA helicase RecQ 3.6.4.12 0.650
4uj5 GNPRas-related protein Rab-11A / 0.650