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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
5fl3 ADP Pili retraction protein PilT

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5fl3 ADPPili retraction protein PilT / 0.877
2ql6 ADPNicotinamide riboside kinase 1 / 0.805
1w5t ANPORC1-type DNA replication protein 2 / 0.786
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.782
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.782
4asu ADPATP synthase subunit alpha, mitochondrial / 0.781
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.780
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.780
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.778
5ftc ADPTPR domain protein / 0.777
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.772
2zr9 DTPProtein RecA / 0.767
4ihq ADPConserved Archaeal protein / 0.766
3uk6 ADPRuvB-like 2 3.6.4.12 0.764
3tqc ADPPantothenate kinase / 0.762
1xmv ADPProtein RecA / 0.761
2qen ADPWalker-Type ATPase / 0.761
2x2r ADPKinesin-like protein KIF11 / 0.761
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.761
2eck ADPAdenylate kinase / 0.760
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.759
2r9v ATPATP synthase subunit alpha / 0.758
4jlo ADPAdenylate kinase / 0.758
5ftf ADPTPR domain protein / 0.758
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.757
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.756
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.755
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.754
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.754
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.754
4jsy GTPMetallophosphoesterase / 0.754
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.754
1tu3 GNPRas-related protein Rab-5A / 0.751
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.750
1zbd GTPRas-related protein Rab-3A / 0.749
2rgx AP5Adenylate kinase / 0.749
2xsz ATPRuvB-like 2 3.6.4.12 0.749
2zts ADPUncharacterized protein / 0.748
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.747
3r9i ADPSeptum site-determining protein MinD / 0.747
4ww4 ADPRuvB-like helicase / 0.747
1fnn ADPORC1-type DNA replication protein / 0.746
2uyi ADPKinesin-like protein KIF11 / 0.746
4qbh AP5Adenylate kinase / 0.746
1zio AP5Adenylate kinase / 0.745
4qbi AP5Adenylate kinase / 0.745
4jl6 ADPAdenylate kinase / 0.744
1mma ADPMyosin-2 heavy chain / 0.743
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.743
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.742
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.742
5aun ADPIron-sulfur cluster carrier protein / 0.742
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.741
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.741
2hld ANPATP synthase subunit alpha, mitochondrial / 0.741
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.741
3k1j ADPATP-dependent protease Lon / 0.741
4cf7 ADPAdenylate kinase / 0.741
4d81 ADPAAA ATPase, central domain protein / 0.741
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.739
1w5t ADPORC1-type DNA replication protein 2 / 0.739
1z2a GDPRas-related protein Rab-23 / 0.739
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.739
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.739
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.739
1t91 GTPRas-related protein Rab-7a / 0.738
2zrj AGSProtein RecA / 0.738
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.738
3tlx ADPAdenylate kinase 2 / 0.738
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.738
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.738
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.738
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.737
1g6o ADPCag alpha / 0.736
1wdt GTPElongation factor G (EF-G-2) / 0.736
4mkh AP5Adenylate kinase / 0.736
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.735
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.735
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.735
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.735
1z0f GDPRas-related protein Rab-14 / 0.732
2fl2 ADPKinesin-like protein KIF11 / 0.732
3mjh GTPRas-related protein Rab-5A / 0.732
3zia ATPATP synthase subunit alpha, mitochondrial / 0.732
4pk4 ADPUnconventional myosin-VI / 0.732
1x1r GDPRas-related protein M-Ras / 0.731
2c9o ADPRuvB-like 1 3.6.4.12 0.731
2pg2 ADPKinesin-like protein KIF11 / 0.731
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.731
4d0l GSPRas-related protein Rab-11A / 0.730
4lv6 GDPGTPase KRas / 0.730
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.729
2cl6 CAGGTPase HRas / 0.729
4jky ADPAdenylate kinase / 0.729
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.729
3c41 ANPAmino acid ABC transporter / 0.728
3d8b ADPFidgetin-like protein 1 3.6.4 0.728
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.728
1p9w ANPType II secretion system protein E / 0.727
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.726
2gm1 ADPKinesin-like protein KIF11 / 0.725
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.724
3l9h ADPKinesin-like protein KIF11 / 0.724
3oee ANPATP synthase subunit alpha, mitochondrial / 0.723
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.723
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.723
1jx2 ADPMyosin-2 heavy chain / 0.722
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.721
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.721
4pjj ADPUnconventional myosin-VI / 0.721
1yra GDPGPN-loop GTPase PAB0955 / 0.720
1z0a GDPRas-related protein Rab-2A / 0.720
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.717
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.716
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.716
2vf7 ADPUvrABC system protein A / 0.716
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.716
4idn GNPAtlastin-1 3.6.5 0.716
4idp GNPAtlastin-1 3.6.5 0.716
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.715
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.715
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.714
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.714
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.713
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.713
4y0v GDPADP-ribosylation factor 1, putative / 0.713
4ylg GDPADP-ribosylation factor 1, putative / 0.713
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.710
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
4o2l GTPGTP-binding protein Rheb / 0.710
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.710
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.710
1ank ANPAdenylate kinase / 0.709
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.709
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.709
3kkq GDPRas-related protein M-Ras / 0.709
4nh0 ATPESX secretion system protein EccC / 0.709
4pjk ADPMyosin-2 heavy chain / 0.709
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.708
3thy ADPDNA mismatch repair protein Msh2 / 0.708
4dsu GDPGTPase KRas / 0.708
2o8b ADPDNA mismatch repair protein Msh2 / 0.707
3t1t GDPProbable gliding protein mglA / 0.707
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.706
3a58 GNPGTP-binding protein RHO1 / 0.706
3hpr AP5Adenylate kinase / 0.706
1xms ANPProtein RecA / 0.705
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.704
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.704
1f5n GNPGuanylate-binding protein 1 / 0.702
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.702
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.701
4goj GNPADP-ribosylation factor-like protein 3 / 0.701
3w3z GTPGTP-binding nuclear protein Ran / 0.700
4hi0 GDPUrease accessory protein UreG / 0.700
1sxj ADPReplication factor C subunit 5 / 0.699
1xtr GNPGTP-binding protein Rheb / 0.699
3oes GNPGTPase RhebL1 / 0.699
4g01 GDPRas-related protein RABF2b / 0.699
1w5s ADPORC1-type DNA replication protein 2 / 0.698
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.698
3q9l ATPSeptum site-determining protein MinD / 0.697
1z0d GDPRas-related protein Rab-5C / 0.696
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.696
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.695
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.695
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.695
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.694
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.694
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.694
4dlt GNPGTPase HRas / 0.693
4ncl GDPEukaryotic translation initiation factor 5B / 0.693
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.692
4qbg AP5Adenylate kinase / 0.692
1zc4 GNPRas-related protein Ral-A / 0.691
3e5h GNPRas-related protein Rab-28 / 0.691
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.690
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.690
3k3b ADPKinesin-like protein KIF11 / 0.689
4tq9 GDPGTPase KRas / 0.689
3a6p GTPGTP-binding nuclear protein Ran / 0.688
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.687
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.687
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.687
4l16 ADPFidgetin-like protein 1 3.6.4 0.687
4v02 ATPSite-determining protein / 0.686
2c96 ATPPsp operon transcriptional activator / 0.685
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.685
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.685
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.685
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.684
2rgb GNPGTPase HRas / 0.684
2rge GNPGTPase HRas / 0.684
3nbx ADPATPase RavA 3.6.3 0.684
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.684
1g17 GNPRas-related protein SEC4 / 0.683
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.683
2rgg GNPGTPase HRas / 0.683
3lbn GNPGTPase HRas / 0.683
4db1 ANPMyosin-7 / 0.683
4hdq GNPRas-related protein Rap-1b / 0.683
2zfi ADPKinesin-like protein KIF1A / 0.682
2zro ADPProtein RecA / 0.682
5fv0 ONAESX secretion system protein EccC / 0.682
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.681
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.681
1yu9 GNPRas-related protein Rab-4A / 0.681
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.681
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.681
4a28 ADPKinesin-like protein KIF11 / 0.681
1z6t ADPApoptotic protease-activating factor 1 / 0.680
2fg5 GNPRas-related protein Rab-31 / 0.680
1uad GNPRas-related protein Ral-A / 0.679
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.679
2vcz VC3Hematopoietic prostaglandin D synthase / 0.679
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
5d3q GDPDynamin-1 3.6.5.5 0.679
2yeg XQGHeat shock protein HSP 90-alpha / 0.678
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.678
3cf0 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.677
3fkq ATPNtrC-like two-domain protein / 0.677
4cym GCPRas-related protein Rab-32 / 0.677
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.676
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.676
3tnf GNPRas-related protein Rab-8A / 0.676
4lhv GDPRas-related protein Rab-8A / 0.676
4tyq AP5Adenylate kinase / 0.676
3kuc GDPRas-related protein Rap-1A / 0.675
3m0e ATPTranscriptional regulator (NtrC family) / 0.674
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.673
3pcr GTPADP-ribosylation factor 6 / 0.673
1ake AP5Adenylate kinase / 0.672
1nly AGSCag alpha / 0.672
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.672
5k5z ANPUncharacterized protein / 0.671
4qm6 GTPMetallophosphoesterase / 0.670
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.669
2jlr ANPGenome polyprotein 3.4.21.91 0.669
2c9c ATPPsp operon transcriptional activator / 0.668
4iok ADPFormate--tetrahydrofolate ligase / 0.668
1svl ADPLarge T antigen 3.6.4 0.667
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.666
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.666
2bc9 GNPGuanylate-binding protein 1 / 0.665
2q2y ADPKinesin-like protein KIF11 / 0.665
4js0 GNPCell division control protein 42 homolog / 0.665
1a4r GNHCell division control protein 42 homolog / 0.664
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.663
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
2ad5 ADPCTP synthase / 0.663
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.663
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.663
4dzz ADPPlasmid partitioning protein ParF / 0.662
4oi2 ADPProtein clpf-1 / 0.662
5da9 AGSUncharacterized protein / 0.662
1d5c GDPGTPase (Rab6) / 0.660
1w7i ADPUnconventional myosin-Va / 0.659
2uz3 TTPThymidine kinase / 0.659
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.657
3aez GDPPantothenate kinase 2.7.1.33 0.657
1v8k ANPKinesin-like protein KIF2C / 0.656
2bme GNPRas-related protein Rab-4A / 0.656
2xae ADPKinesin-like protein KIF11 / 0.656
1e0j ANPDNA primase/helicase 2.7.7 0.655
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.655
4iei ADPGene 2 protein / 0.655
4xgu ADPPutative pachytene checkpoint protein 2 / 0.654
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.653
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.653
4kod ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.653
4o3m ADPBloom syndrome protein 3.6.4.12 0.653
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.652
1p3j AP5Adenylate kinase / 0.652
1b7t ADPMyosin heavy chain, striated muscle / 0.651
1ii6 ADPKinesin-like protein KIF11 / 0.651
1wa5 GTPGTP-binding nuclear protein Ran / 0.651
3law GNPRas-related protein Rab-7a / 0.651
1k5d GNPGTP-binding nuclear protein Ran / 0.650