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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
2vos ADP Folylpolyglutamate synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2vos ADPFolylpolyglutamate synthase / 1.096
2vor ACPFolylpolyglutamate synthase / 0.979
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.949
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.841
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.792
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.785
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.780
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.773
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.771
4l9w GNPGTPase HRas / 0.742
3rs7 GNPGTPase HRas / 0.734
3oiv GNPGTPase HRas / 0.733
3oiw GNPGTPase HRas / 0.733
3rs0 GNPGTPase HRas / 0.733
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.730
3i3s GNPGTPase HRas / 0.729
3k8y GNPGTPase HRas / 0.729
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.727
3l1c ADPProtein claret segregational / 0.725
4lhw GNPRas-related protein Rab-8A / 0.721
2rgb GNPGTPase HRas / 0.720
2rge GNPGTPase HRas / 0.719
3oiu GNPGTPase HRas / 0.719
3rs5 GNPGTPase HRas / 0.719
3rsl GNPGTPase HRas / 0.719
3v4f GNPGTPase HRas / 0.719
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.718
3rs4 GNPGTPase HRas / 0.718
4dlt GNPGTPase HRas / 0.718
4dlw GNPGTPase HRas / 0.718
4hdo GNPRas-related protein Rap-1b / 0.718
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.717
4jl5 ADPAdenylate kinase / 0.715
4dls GNPGTPase HRas / 0.714
4dlv GNPGTPase HRas / 0.714
3l8y GNPGTPase HRas / 0.713
3lbi GNPGTPase HRas / 0.713
3lbn GNPGTPase HRas / 0.713
4cf7 ADPAdenylate kinase / 0.713
5b2z GNPGTPase HRas / 0.713
1z2a GDPRas-related protein Rab-23 / 0.711
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.710
4g0n GNPGTPase HRas / 0.710
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.709
1xmv ADPProtein RecA / 0.709
3r9i ADPSeptum site-determining protein MinD / 0.708
3tlx ADPAdenylate kinase 2 / 0.708
5ftc ADPTPR domain protein / 0.708
1mma ADPMyosin-2 heavy chain / 0.707
2eck ADPAdenylate kinase / 0.707
3ddc GNPGTPase HRas / 0.707
3pit GNPRas-related protein M-Ras / 0.707
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.705
1s1c GNPTransforming protein RhoA / 0.703
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.702
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.700
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.698
3rab GNPRas-related protein Rab-3A / 0.698
2bbw GP5Adenylate kinase 4, mitochondrial / 0.697
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.697
4jl6 ADPAdenylate kinase / 0.697
2fl2 ADPKinesin-like protein KIF11 / 0.695
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.694
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.694
1kmq GNPTransforming protein RhoA / 0.694
4jld ADPAdenylate kinase / 0.694
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.693
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.693
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.693
4jsy GTPMetallophosphoesterase / 0.693
1sdm ADPKinesin heavy chain-like protein / 0.691
2gcp GSPRho-related GTP-binding protein RhoC / 0.691
4iok ADPFormate--tetrahydrofolate ligase / 0.691
2dpx GDPGTP-binding protein RAD / 0.690
2y65 ADPKinesin heavy chain / 0.690
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.689
3q9l ATPSeptum site-determining protein MinD / 0.689
4rkf GNPRas-related protein Rab-3 / 0.689
1yrs ADPKinesin-like protein KIF11 / 0.688
2ql6 ADPNicotinamide riboside kinase 1 / 0.688
5bn3 ADPV-type ATP synthase alpha chain / 0.688
5bn3 ADPNEQ263 / 0.688
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.686
2x2r ADPKinesin-like protein KIF11 / 0.685
4jky ADPAdenylate kinase / 0.685
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.684
3lbh GNPGTPase HRas / 0.684
3x1z GNPRas-related protein Rap-1b / 0.684
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.684
1p9w ANPType II secretion system protein E / 0.683
1z2c GNPRho-related GTP-binding protein RhoC / 0.682
3law GNPRas-related protein Rab-7a / 0.682
2fna ADPUncharacterized protein / 0.681
3qbv GDPCell division control protein 42 homolog / 0.681
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.680
4asu ADPATP synthase subunit alpha, mitochondrial / 0.680
5c46 GSPRas-related protein Rab-11A / 0.680
1wbb ADPDNA mismatch repair protein MutS / 0.679
5ftf ADPTPR domain protein / 0.679
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.678
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.678
3tqc ADPPantothenate kinase / 0.678
4hi0 GDPUrease accessory protein UreG / 0.678
4qos ADPPsp operon transcriptional activator / 0.678
4uj3 GNPRas-related protein Rab-11A / 0.678
1ii6 ADPKinesin-like protein KIF11 / 0.677
2bme GNPRas-related protein Rab-4A / 0.677
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.677
4i1v ADPDephospho-CoA kinase / 0.676
2j5x GSPADP-ribosylation factor 6 / 0.675
1sq5 ADPPantothenate kinase 2.7.1.33 0.674
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.674
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.674
4jlo ADPAdenylate kinase / 0.674
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.674
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.672
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.672
1xtr GNPGTP-binding protein Rheb / 0.672
1w5s ADPORC1-type DNA replication protein 2 / 0.671
2zr9 DTPProtein RecA / 0.671
1l8q ADPChromosomal replication initiator protein DnaA / 0.670
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.670
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.670
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.669
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.668
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
1d5c GDPGTPase (Rab6) / 0.667
1svl ADPLarge T antigen 3.6.4 0.667
4lpk GDPGTPase KRas / 0.667
3b1x GNPFerrous iron transport protein B / 0.666
2bc9 GNPGuanylate-binding protein 1 / 0.665
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.665
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.664
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.664
3bxz ADPProtein translocase subunit SecA / 0.664
4ihq ADPConserved Archaeal protein / 0.664
4nl4 ADPPrimosomal protein N' / 0.664
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.663
1k5d GNPGTP-binding nuclear protein Ran / 0.662
1w5t ANPORC1-type DNA replication protein 2 / 0.662
3eg5 GNPCell division control protein 42 homolog / 0.661
4pjj ADPUnconventional myosin-VI / 0.661
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.660
4xvu ATPATPase GET3 / 0.660
1vg8 GNPRas-related protein Rab-7a / 0.659
2e91 ZOLGeranylgeranyl pyrophosphate synthase / 0.659
2o8b ADPDNA mismatch repair protein Msh2 / 0.659
4uj5 GNPRas-related protein Rab-11A / 0.659
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.658
4ol0 GTPGTP-binding nuclear protein Ran / 0.658
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.657
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.655
2uyi ADPKinesin-like protein KIF11 / 0.654
4rz3 ADPSite-determining protein / 0.654
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.653
1z6t ADPApoptotic protease-activating factor 1 / 0.653
4ohx ADPProtein clpf-1 / 0.653
4a28 ADPKinesin-like protein KIF11 / 0.652
4dxa GSPRas-related protein Rap-1b / 0.652
1p7c T5AThymidine kinase / 0.650
4gvz ADPArginine kinase 2.7.3.3 0.650