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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
5ftf ADP TPR domain protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5ftf ADPTPR domain protein / 0.959
5ftc ADPTPR domain protein / 0.802
5fl3 ADPPili retraction protein PilT / 0.758
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.750
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.750
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.737
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.734
2ql6 ADPNicotinamide riboside kinase 1 / 0.732
2fna ADPUncharacterized protein / 0.730
1g6o ADPCag alpha / 0.729
2ffq GSPRas-related protein Rab-6B / 0.726
3oee ANPATP synthase subunit alpha, mitochondrial / 0.722
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.722
4pk4 ADPUnconventional myosin-VI / 0.721
4qm6 GTPMetallophosphoesterase / 0.721
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.720
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.718
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.718
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.718
1zio AP5Adenylate kinase / 0.717
4mkh AP5Adenylate kinase / 0.717
2eck ADPAdenylate kinase / 0.716
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.716
1xmv ADPProtein RecA / 0.713
4gp6 ADPMetallophosphoesterase / 0.712
1z6t ADPApoptotic protease-activating factor 1 / 0.710
4ike ADPAdenylate kinase / 0.710
3zia ATPATP synthase subunit alpha, mitochondrial / 0.709
4jld ADPAdenylate kinase / 0.709
1ny5 ADPTranscriptional regulator (NtrC family) / 0.707
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.707
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.706
4d0l GSPRas-related protein Rab-11A / 0.706
4ww4 ADPRuvB-like helicase / 0.706
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.704
4lrw GDPGTPase KRas / 0.704
5aun ADPIron-sulfur cluster carrier protein / 0.704
3a6p GTPGTP-binding nuclear protein Ran / 0.701
2x7e ADPKinesin-like protein KIF11 / 0.700
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.700
3tkl GTPRas-related protein Rab-1A / 0.700
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.699
2pg2 ADPKinesin-like protein KIF11 / 0.699
3kz1 GSPTransforming protein RhoA / 0.699
4o2l GTPGTP-binding protein Rheb / 0.699
1mmg AGSMyosin-2 heavy chain / 0.698
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.697
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.697
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.696
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.696
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.695
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
1wdt GTPElongation factor G (EF-G-2) / 0.695
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.694
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.694
1l8q ADPChromosomal replication initiator protein DnaA / 0.693
1z0a GDPRas-related protein Rab-2A / 0.692
4b7b ADPKinesin-like protein KIF11 / 0.692
4dvg GSPRho family GTPase / 0.692
3tqc ADPPantothenate kinase / 0.691
3w3z GTPGTP-binding nuclear protein Ran / 0.691
4itr GDPCell division control protein 42 homolog / 0.691
4jky ADPAdenylate kinase / 0.691
3l9h ADPKinesin-like protein KIF11 / 0.690
4pfp ADPUnconventional myosin-VI / 0.690
4pjk ADPMyosin-2 heavy chain / 0.690
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.689
1sq5 ADPPantothenate kinase 2.7.1.33 0.689
2fe4 GDPRas-related protein Rab-6B / 0.689
4jl6 ADPAdenylate kinase / 0.689
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.688
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
1g16 GDPRas-related protein SEC4 / 0.688
4pjj ADPUnconventional myosin-VI / 0.688
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.687
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.687
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.687
4jlo ADPAdenylate kinase / 0.687
4lpk GDPGTPase KRas / 0.687
1ank ANPAdenylate kinase / 0.686
1zbd GTPRas-related protein Rab-3A / 0.686
3oes GNPGTPase RhebL1 / 0.686
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.686
4hi0 GDPUrease accessory protein UreG / 0.686
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.685
4g01 GDPRas-related protein RABF2b / 0.685
1cxz GSPTransforming protein RhoA / 0.684
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.684
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.684
3uk6 ADPRuvB-like 2 3.6.4.12 0.684
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.684
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.684
1m7b GTPRho-related GTP-binding protein RhoE / 0.683
2x2r ADPKinesin-like protein KIF11 / 0.683
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.683
4asu ADPATP synthase subunit alpha, mitochondrial / 0.683
1sxj ADPReplication factor C subunit 5 / 0.682
2uyi ADPKinesin-like protein KIF11 / 0.682
2y65 ADPKinesin heavy chain / 0.682
4i1v ADPDephospho-CoA kinase / 0.682
4uj5 GNPRas-related protein Rab-11A / 0.682
4xsg GSPTransforming protein RhoA / 0.682
2vos ADPFolylpolyglutamate synthase / 0.679
3c41 ANPAmino acid ABC transporter / 0.679
3ea5 GDPGTP-binding nuclear protein Ran / 0.679
1z0d GDPRas-related protein Rab-5C / 0.678
2gm1 ADPKinesin-like protein KIF11 / 0.678
4jsy GTPMetallophosphoesterase / 0.678
4kvg GTPRas-related protein Rap-1A / 0.678
5c46 GSPRas-related protein Rab-11A / 0.678
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.677
1wbb ADPDNA mismatch repair protein MutS / 0.677
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.677
4dso GSPGTPase KRas / 0.677
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.677
4ihq ADPConserved Archaeal protein / 0.677
2zfi ADPKinesin-like protein KIF1A / 0.676
4y0v GDPADP-ribosylation factor 1, putative / 0.676
4ylg GDPADP-ribosylation factor 1, putative / 0.676
2bku GTPGTP-binding nuclear protein Ran / 0.675
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.675
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.675
3law GNPRas-related protein Rab-7a / 0.675
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.675
3cob ADPKinesin heavy chain-like protein / 0.674
4iei ADPGene 2 protein / 0.674
4iok ADPFormate--tetrahydrofolate ligase / 0.674
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.673
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.673
1yra GDPGPN-loop GTPase PAB0955 / 0.673
2ad5 ADPCTP synthase / 0.673
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.673
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.673
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.673
4a51 ADPKinesin-like protein KIF11 / 0.673
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.672
3k1j ADPATP-dependent protease Lon / 0.672
4jjz ADPFormate--tetrahydrofolate ligase / 0.672
1jx2 ADPMyosin-2 heavy chain / 0.671
1w5t ANPORC1-type DNA replication protein 2 / 0.671
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.671
1zc3 GNPRas-related protein Ral-A / 0.671
2zrj AGSProtein RecA / 0.671
4lhv GDPRas-related protein Rab-8A / 0.671
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.671
4o25 GTPGTP-binding protein Rheb / 0.671
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.671
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.671
1uad GNPRas-related protein Ral-A / 0.670
4zca ADPKinesin-like protein KIF11 / 0.670
1p9w ANPType II secretion system protein E / 0.669
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.669
1yrs ADPKinesin-like protein KIF11 / 0.669
1z2a GDPRas-related protein Rab-23 / 0.669
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.669
3r9i ADPSeptum site-determining protein MinD / 0.669
4a1z ADPKinesin-like protein KIF11 / 0.669
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.669
5dif GNPGTP-binding nuclear protein Ran / 0.669
5k5z ANPUncharacterized protein / 0.669
1am4 GNPCell division control protein 42 homolog / 0.668
1b7t ADPMyosin heavy chain, striated muscle / 0.668
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.668
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.668
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.667
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.667
3myk ANPMyosin-2 heavy chain / 0.667
4idn GNPAtlastin-1 3.6.5 0.667
4jl5 ADPAdenylate kinase / 0.667
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.667
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.666
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.666
2dpx GDPGTP-binding protein RAD / 0.666
3bbp GTPRas-related protein Rab-6A / 0.666
3ieu GDPGTPase Era / 0.666
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.665
4db1 ANPMyosin-7 / 0.665
4ncl GDPEukaryotic translation initiation factor 5B / 0.665
4ohv ANPProtein clpf-1 / 0.665
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.665
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.664
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
2o8b ADPDNA mismatch repair protein Msh2 / 0.664
3ref GDPRho family GTPase / 0.664
4qxa GTPRas-related protein Rab-9A / 0.664
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.663
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.663
4luc GDPGTPase KRas / 0.663
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.662
1d5c GDPGTPase (Rab6) / 0.661
1s1c GNPTransforming protein RhoA / 0.661
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.661
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.661
3x1w GDPRas-related protein Rap-1b / 0.661
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.661
1lfd GNPGTPase HRas / 0.660
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.660
2uz3 TTPThymidine kinase / 0.660
4js0 GNPCell division control protein 42 homolog / 0.660
4uj3 GNPRas-related protein Rab-11A / 0.660
2rgb GNPGTPase HRas / 0.659
2rge GNPGTPase HRas / 0.659
3lbh GNPGTPase HRas / 0.659
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.658
3ddc GNPGTPase HRas / 0.658
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.658
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.658
3oiv GNPGTPase HRas / 0.658
4lhw GNPRas-related protein Rab-8A / 0.658
5da9 AGSUncharacterized protein / 0.658
3kko GNPRas-related protein M-Ras / 0.657
1yu9 GNPRas-related protein Rab-4A / 0.656
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.655
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.654
3ung ADPCRISPR system Cmr subunit Cmr2 / 0.654
1tu3 GNPRas-related protein Rab-5A / 0.653
1xtr GNPGTP-binding protein Rheb / 0.653
2hld ANPATP synthase subunit alpha, mitochondrial / 0.653
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
3eg5 GNPCell division control protein 42 homolog / 0.653
3pcr GTPADP-ribosylation factor 6 / 0.652
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.652
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.652
1w5s ADPORC1-type DNA replication protein 2 / 0.651
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.651
3cph GDPRas-related protein SEC4 / 0.651
3t1t GDPProbable gliding protein mglA / 0.651
4xvq GNPGTPase HRas / 0.651
4yqf GDPSeptin-9 / 0.651
2c9o ADPRuvB-like 1 3.6.4.12 0.650
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.650