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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
4zca ADP Kinesin-like protein KIF11

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4zca ADPKinesin-like protein KIF11 / 1.017
3k3b ADPKinesin-like protein KIF11 / 0.853
1sdm ADPKinesin heavy chain-like protein / 0.842
1ii6 ADPKinesin-like protein KIF11 / 0.840
2xae ADPKinesin-like protein KIF11 / 0.838
2x2r ADPKinesin-like protein KIF11 / 0.814
2pg2 ADPKinesin-like protein KIF11 / 0.810
2g1q ADPKinesin-like protein KIF11 / 0.807
2uyi ADPKinesin-like protein KIF11 / 0.807
2fl2 ADPKinesin-like protein KIF11 / 0.805
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.798
4a1z ADPKinesin-like protein KIF11 / 0.798
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.795
2qen ADPWalker-Type ATPase / 0.795
2x7e ADPKinesin-like protein KIF11 / 0.794
4b7b ADPKinesin-like protein KIF11 / 0.791
3l9h ADPKinesin-like protein KIF11 / 0.790
1yrs ADPKinesin-like protein KIF11 / 0.789
2y65 ADPKinesin heavy chain / 0.789
4a28 ADPKinesin-like protein KIF11 / 0.786
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.784
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.780
2gm1 ADPKinesin-like protein KIF11 / 0.778
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.777
4asu ADPATP synthase subunit alpha, mitochondrial / 0.777
4lpk GDPGTPase KRas / 0.777
4itr GDPCell division control protein 42 homolog / 0.776
1xmv ADPProtein RecA / 0.775
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.772
4lrw GDPGTPase KRas / 0.770
4l8g GDPGTPase KRas / 0.769
3kkq GDPRas-related protein M-Ras / 0.766
4obe GDPGTPase KRas / 0.766
4epw GDPGTPase KRas / 0.765
4l9s GDPGTPase HRas / 0.765
1x1r GDPRas-related protein M-Ras / 0.763
2ce2 GDPGTPase HRas / 0.763
4q02 GDPGTPase KRas / 0.763
4ql3 GDPGTPase KRas / 0.763
5aun ADPIron-sulfur cluster carrier protein / 0.763
1z2a GDPRas-related protein Rab-23 / 0.762
2fe4 GDPRas-related protein Rab-6B / 0.762
3cob ADPKinesin heavy chain-like protein / 0.762
3kud GDPGTPase HRas / 0.762
4epx GDPGTPase KRas / 0.762
4ldj GDPGTPase KRas / 0.762
4q03 GDPGTPase KRas / 0.762
4tq9 GDPGTPase KRas / 0.762
1l8q ADPChromosomal replication initiator protein DnaA / 0.761
2dpx GDPGTP-binding protein RAD / 0.761
3kuc GDPRas-related protein Rap-1A / 0.761
3x1w GDPRas-related protein Rap-1b / 0.761
4dsu GDPGTPase KRas / 0.761
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.760
4wa7 GDPGTPase KRas / 0.760
4z54 GDPNeuronal-specific septin-3 / 0.760
5ftc ADPTPR domain protein / 0.758
4dso GSPGTPase KRas / 0.757
4qxa GTPRas-related protein Rab-9A / 0.757
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.756
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.756
2fna ADPUncharacterized protein / 0.756
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.754
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.754
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.753
4lhv GDPRas-related protein Rab-8A / 0.753
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.750
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.750
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.750
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.749
3uk6 ADPRuvB-like 2 3.6.4.12 0.749
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.748
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.748
4lv6 GDPGTPase KRas / 0.748
4xsg GSPTransforming protein RhoA / 0.748
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.747
4luc GDPGTPase KRas / 0.747
4ihq ADPConserved Archaeal protein / 0.746
4yqf GDPSeptin-9 / 0.746
1cxz GSPTransforming protein RhoA / 0.745
3l1c ADPProtein claret segregational / 0.745
3tlx ADPAdenylate kinase 2 / 0.745
4qm6 GTPMetallophosphoesterase / 0.745
1w5t ANPORC1-type DNA replication protein 2 / 0.744
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.744
4xoi GTPTransforming protein RhoA / 0.744
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.743
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.740
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.740
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.739
2rgx AP5Adenylate kinase / 0.738
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.737
3thy ADPDNA mismatch repair protein Msh2 / 0.737
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.736
2r9v ATPATP synthase subunit alpha / 0.736
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.736
1fnn ADPORC1-type DNA replication protein / 0.735
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.735
4jjz ADPFormate--tetrahydrofolate ligase / 0.735
1oix GDPRas-related protein Rab-11A / 0.734
1w5t ADPORC1-type DNA replication protein 2 / 0.734
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.734
3zia ATPATP synthase subunit alpha, mitochondrial / 0.732
1z0d GDPRas-related protein Rab-5C / 0.730
2zfi ADPKinesin-like protein KIF1A / 0.730
3tqc ADPPantothenate kinase / 0.730
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.730
4pk4 ADPUnconventional myosin-VI / 0.730
1t91 GTPRas-related protein Rab-7a / 0.729
2l0x GDPGTP-binding protein Rheb / 0.729
2rgg GNPGTPase HRas / 0.728
4hi0 GDPUrease accessory protein UreG / 0.728
4o2r GDPGTP-binding protein Rheb / 0.728
4pfp ADPUnconventional myosin-VI / 0.728
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.727
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.727
4hdq GNPRas-related protein Rap-1b / 0.727
4o2l GTPGTP-binding protein Rheb / 0.727
1sq5 ADPPantothenate kinase 2.7.1.33 0.726
2gil GTPRas-related protein Rab-6A / 0.726
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.726
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.726
3k9l GNPGTPase HRas / 0.725
3myk ANPMyosin-2 heavy chain / 0.725
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.725
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.725
2q2z ADPKinesin-like protein KIF11 / 0.724
4d0l GSPRas-related protein Rab-11A / 0.724
4dvg GSPRho family GTPase / 0.724
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.723
3kz1 GSPTransforming protein RhoA / 0.723
4gp6 ADPMetallophosphoesterase / 0.723
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.722
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.722
4a51 ADPKinesin-like protein KIF11 / 0.722
4g01 GDPRas-related protein RABF2b / 0.722
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.722
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.721
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.721
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.721
4dzz ADPPlasmid partitioning protein ParF / 0.721
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.720
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.720
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.719
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.719
3ftq GNPSeptin-2 / 0.719
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.719
1f5n GNPGuanylate-binding protein 1 / 0.718
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.718
2zr9 DTPProtein RecA / 0.718
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.717
1am4 GNPCell division control protein 42 homolog / 0.716
1mmg AGSMyosin-2 heavy chain / 0.716
4pjk ADPMyosin-2 heavy chain / 0.716
1z0f GDPRas-related protein Rab-14 / 0.715
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.715
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.714
1mma ADPMyosin-2 heavy chain / 0.714
1nly AGSCag alpha / 0.714
2gcp GSPRho-related GTP-binding protein RhoC / 0.714
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.714
2q2y ADPKinesin-like protein KIF11 / 0.714
5c46 GSPRas-related protein Rab-11A / 0.714
1m7b GTPRho-related GTP-binding protein RhoE / 0.713
4pjj ADPUnconventional myosin-VI / 0.713
4y0v GDPADP-ribosylation factor 1, putative / 0.713
1xms ANPProtein RecA / 0.712
3m0e ATPTranscriptional regulator (NtrC family) / 0.712
4ncl GDPEukaryotic translation initiation factor 5B / 0.712
1wbb ADPDNA mismatch repair protein MutS / 0.711
2ffq GSPRas-related protein Rab-6B / 0.711
4d81 ADPAAA ATPase, central domain protein / 0.711
4xvq GNPGTPase HRas / 0.711
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.710
4kvg GTPRas-related protein Rap-1A / 0.710
3ea5 GDPGTP-binding nuclear protein Ran / 0.709
3hqd ANPKinesin-like protein KIF11 / 0.709
3mjh GTPRas-related protein Rab-5A / 0.709
4ap0 ADPKinesin-like protein KIF11 / 0.709
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.709
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.709
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.709
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.708
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.707
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.707
1jx2 ADPMyosin-2 heavy chain / 0.706
1v8k ANPKinesin-like protein KIF2C / 0.706
2bku GTPGTP-binding nuclear protein Ran / 0.706
2cls GTPRho-related GTP-binding protein Rho6 / 0.706
3cph GDPRas-related protein SEC4 / 0.706
1uad GNPRas-related protein Ral-A / 0.705
2zts ADPUncharacterized protein / 0.705
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.705
3tkl GTPRas-related protein Rab-1A / 0.705
4mkh AP5Adenylate kinase / 0.705
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.704
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.704
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.704
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.704
4ys0 ADPProtein translocase subunit SecA / 0.704
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.703
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.703
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.703
1ny5 ADPTranscriptional regulator (NtrC family) / 0.702
4oi2 ADPProtein clpf-1 / 0.702
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.701
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.700
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.700
3k1j ADPATP-dependent protease Lon / 0.700
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.700
4mkf AP5Adenylate kinase / 0.700
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.699
1p9w ANPType II secretion system protein E / 0.699
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.699
2xsz ATPRuvB-like 2 3.6.4.12 0.699
2zrj AGSProtein RecA / 0.699
4jsy GTPMetallophosphoesterase / 0.699
2jlr ANPGenome polyprotein 3.4.21.91 0.698
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.698
2hld ANPATP synthase subunit alpha, mitochondrial / 0.697
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.697
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.697
1n6m ADPProtein claret segregational / 0.696
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.696
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.696
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.696
4v02 ATPSite-determining protein / 0.696
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.695
1gwn GTPRho-related GTP-binding protein RhoE / 0.695
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.695
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.695
4nh0 ATPESX secretion system protein EccC / 0.695
3qbt GNPRas-related protein Rab-8A / 0.694
5bn3 ADPV-type ATP synthase alpha chain / 0.694
5bn3 ADPNEQ263 / 0.694
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.693
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.693
4cf7 ADPAdenylate kinase / 0.693
4x8o AP5Adenylate kinase / 0.693
1yra GDPGPN-loop GTPase PAB0955 / 0.691
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.691
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.691
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.690
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.689
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.688
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.688
4tyq AP5Adenylate kinase / 0.688
1ow3 GDPTransforming protein RhoA / 0.687
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.687
1b7t ADPMyosin heavy chain, striated muscle / 0.686
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.686
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.686
2ql6 ADPNicotinamide riboside kinase 1 / 0.686
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.685
5cyo GDPSeptin-9 / 0.685
1xts GTPGTP-binding protein Rheb / 0.684
2uz3 TTPThymidine kinase / 0.684
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.684
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.683
3r9i ADPSeptum site-determining protein MinD / 0.683
4iei ADPGene 2 protein / 0.683
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.683
4xvu ATPATPase GET3 / 0.683
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.681
3c41 ANPAmino acid ABC transporter / 0.680
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.680
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.679
2zrf DTPProtein RecA / 0.679
1ank ANPAdenylate kinase / 0.678
1rrg GDPADP-ribosylation factor 1 / 0.678
2qaj AP5Adenylate kinase / 0.677
4ohx ADPProtein clpf-1 / 0.677
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.677
3oee ANPATP synthase subunit alpha, mitochondrial / 0.676
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
1a2b GSPTransforming protein RhoA / 0.675
1g16 GDPRas-related protein SEC4 / 0.675
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.675
3sop GDPNeuronal-specific septin-3 / 0.675
1sxj ADPReplication factor C subunit 5 / 0.673
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.673
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.673
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.673
2o8b ADPDNA mismatch repair protein Msh2 / 0.672
4ike ADPAdenylate kinase / 0.672
4o25 GTPGTP-binding protein Rheb / 0.672
2iut AGSDNA translocase FtsK / 0.671
3pcr GTPADP-ribosylation factor 6 / 0.671
4jld ADPAdenylate kinase / 0.671
1g6o ADPCag alpha / 0.670
5ftf ADPTPR domain protein / 0.670
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.669
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.668
3qbv GDPCell division control protein 42 homolog / 0.668
3a6p GTPGTP-binding nuclear protein Ran / 0.667
3ea0 ATPATPase, ParA family / 0.667
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.666
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.666
5cyp GSPSeptin-9 / 0.666
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.665
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.665
2dft ADPShikimate kinase 2.7.1.71 0.664
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.664
3aez GDPPantothenate kinase 2.7.1.33 0.664
5k5z ANPUncharacterized protein / 0.664
4i1v ADPDephospho-CoA kinase / 0.662
5d3q GDPDynamin-1 3.6.5.5 0.662
2whx ADPGenome polyprotein 3.4.21.91 0.661
4db1 ANPMyosin-7 / 0.661
2xtn GTPGTPase IMAP family member 2 / 0.660
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.659
3qe0 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.658
4cym GCPRas-related protein Rab-32 / 0.658
1fmw ATPMyosin-2 heavy chain / 0.657
5da9 AGSUncharacterized protein / 0.657
4ww4 ADPRuvB-like helicase / 0.656
1e0j ANPDNA primase/helicase 2.7.7 0.655
1rj9 GCPSignal recognition particle receptor FtsY / 0.655
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.654
4jky ADPAdenylate kinase / 0.654
4qbi AP5Adenylate kinase / 0.654
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.653
5dac AGSUncharacterized protein / 0.653
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.652
2aky AP5Adenylate kinase / 0.650
3q5d GDPAtlastin-1 3.6.5 0.650
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.650
4rz3 ADPSite-determining protein / 0.650