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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
2vor ACP Folylpolyglutamate synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2vor ACPFolylpolyglutamate synthase / 1.079
2vos ADPFolylpolyglutamate synthase / 0.979
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.902
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.892
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.816
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.815
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.776
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.771
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.750
3rab GNPRas-related protein Rab-3A / 0.737
2zr9 DTPProtein RecA / 0.734
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.733
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.725
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.724
3rs4 GNPGTPase HRas / 0.724
2rgb GNPGTPase HRas / 0.721
2rge GNPGTPase HRas / 0.721
3ddc GNPGTPase HRas / 0.721
3kko GNPRas-related protein M-Ras / 0.721
3l8y GNPGTPase HRas / 0.721
3lbh GNPGTPase HRas / 0.721
3oiu GNPGTPase HRas / 0.721
3v4f GNPGTPase HRas / 0.721
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.721
4dls GNPGTPase HRas / 0.721
4dlw GNPGTPase HRas / 0.721
4jld ADPAdenylate kinase / 0.721
4l9w GNPGTPase HRas / 0.721
5b2z GNPGTPase HRas / 0.721
3i3s GNPGTPase HRas / 0.720
3k8y GNPGTPase HRas / 0.720
3lbn GNPGTPase HRas / 0.720
3oiv GNPGTPase HRas / 0.720
3oiw GNPGTPase HRas / 0.720
3pit GNPRas-related protein M-Ras / 0.720
3rs0 GNPGTPase HRas / 0.720
3rs5 GNPGTPase HRas / 0.720
3rs7 GNPGTPase HRas / 0.720
3rsl GNPGTPase HRas / 0.720
4dlt GNPGTPase HRas / 0.720
4dlv GNPGTPase HRas / 0.720
4dlz GNPGTPase HRas / 0.720
4hdo GNPRas-related protein Rap-1b / 0.720
5bn3 ADPV-type ATP synthase alpha chain / 0.720
5bn3 ADPNEQ263 / 0.720
2rgc GNPGTPase HRas / 0.719
3lbi GNPGTPase HRas / 0.719
4dlx GNPGTPase HRas / 0.719
4lhw GNPRas-related protein Rab-8A / 0.719
3x1z GNPRas-related protein Rap-1b / 0.718
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.715
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.715
2zts ADPUncharacterized protein / 0.714
4z54 GDPNeuronal-specific septin-3 / 0.713
3tlx ADPAdenylate kinase 2 / 0.712
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.710
4jl5 ADPAdenylate kinase / 0.708
4jl6 ADPAdenylate kinase / 0.708
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.707
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.707
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.707
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.706
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.706
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.706
4jlo ADPAdenylate kinase / 0.706
3l1c ADPProtein claret segregational / 0.705
3tqc ADPPantothenate kinase / 0.705
4cf7 ADPAdenylate kinase / 0.705
4jsy GTPMetallophosphoesterase / 0.705
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.703
2eck ADPAdenylate kinase / 0.702
3vhx GTPADP-ribosylation factor 6 / 0.702
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.701
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.701
5dif GNPGTP-binding nuclear protein Ran / 0.701
1oix GDPRas-related protein Rab-11A / 0.700
4pjk ADPMyosin-2 heavy chain / 0.700
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.699
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.699
4rkf GNPRas-related protein Rab-3 / 0.699
1z2a GDPRas-related protein Rab-23 / 0.698
1w5s ADPORC1-type DNA replication protein 2 / 0.697
2fna ADPUncharacterized protein / 0.697
4ike ADPAdenylate kinase / 0.697
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.696
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.696
4pk4 ADPUnconventional myosin-VI / 0.696
4idp GNPAtlastin-1 3.6.5 0.695
4ihq ADPConserved Archaeal protein / 0.695
2bme GNPRas-related protein Rab-4A / 0.694
4jjz ADPFormate--tetrahydrofolate ligase / 0.694
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.694
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.693
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.692
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.692
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.692
1z0d GDPRas-related protein Rab-5C / 0.692
1kmq GNPTransforming protein RhoA / 0.690
1s1c GNPTransforming protein RhoA / 0.690
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.689
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.688
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.688
3e5h GNPRas-related protein Rab-28 / 0.688
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.688
4js0 GNPCell division control protein 42 homolog / 0.688
1n6l GTPRas-related protein Rab-5A / 0.686
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.686
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.685
5di3 GNPADP-ribosylation factor-like protein 3 / 0.685
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.684
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.684
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.684
4cym GCPRas-related protein Rab-32 / 0.684
2q2z ADPKinesin-like protein KIF11 / 0.683
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.683
2y65 ADPKinesin heavy chain / 0.682
1fnn ADPORC1-type DNA replication protein / 0.681
1svm ATPLarge T antigen 3.6.4 0.681
3thy ADPDNA mismatch repair protein Msh2 / 0.681
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.680
2bku GTPGTP-binding nuclear protein Ran / 0.679
3myk ANPMyosin-2 heavy chain / 0.678
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.677
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.677
2c9o ADPRuvB-like 1 3.6.4.12 0.675
3k1j ADPATP-dependent protease Lon / 0.675
4i1v ADPDephospho-CoA kinase / 0.675
4xsg GSPTransforming protein RhoA / 0.675
1ky2 GNPGTP-binding protein YPT7 / 0.674
1sq5 ADPPantothenate kinase 2.7.1.33 0.674
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.674
4jky ADPAdenylate kinase / 0.674
4ys0 ADPProtein translocase subunit SecA / 0.674
1ii6 ADPKinesin-like protein KIF11 / 0.673
2fl2 ADPKinesin-like protein KIF11 / 0.673
2gcp GSPRho-related GTP-binding protein RhoC / 0.673
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.673
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.673
3oes GNPGTPase RhebL1 / 0.673
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.673
5aun ADPIron-sulfur cluster carrier protein / 0.673
5k5z ANPUncharacterized protein / 0.673
1okk GCPSignal recognition particle protein / 0.672
1okk GCPSignal recognition particle receptor FtsY / 0.672
4hse ADPChaperone protein ClpB / 0.672
2e91 ZOLGeranylgeranyl pyrophosphate synthase / 0.671
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.671
4pjj ADPUnconventional myosin-VI / 0.671
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.670
2j7p GNPSignal recognition particle protein / 0.670
2j7p GNPSignal recognition particle receptor FtsY / 0.670
3law GNPRas-related protein Rab-7a / 0.670
4rz3 ADPSite-determining protein / 0.669
1wbb ADPDNA mismatch repair protein MutS / 0.668
1yrs ADPKinesin-like protein KIF11 / 0.668
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.668
2pg2 ADPKinesin-like protein KIF11 / 0.668
2uyi ADPKinesin-like protein KIF11 / 0.668
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.668
4b7b ADPKinesin-like protein KIF11 / 0.668
4dvg GSPRho family GTPase / 0.668
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
2x7e ADPKinesin-like protein KIF11 / 0.667
3l9h ADPKinesin-like protein KIF11 / 0.667
1rrg GDPADP-ribosylation factor 1 / 0.666
3ftq GNPSeptin-2 / 0.666
1ibr GNPGTP-binding nuclear protein Ran / 0.665
1l8q ADPChromosomal replication initiator protein DnaA / 0.664
1w5t ANPORC1-type DNA replication protein 2 / 0.664
1w5t ADPORC1-type DNA replication protein 2 / 0.664
2fg5 GNPRas-related protein Rab-31 / 0.664
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.663
4mit GTPRho-related protein racC / 0.663
5c46 GSPRas-related protein Rab-11A / 0.663
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.662
4uj3 GNPRas-related protein Rab-11A / 0.662
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.661
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
3r9i ADPSeptum site-determining protein MinD / 0.661
4y0v GDPADP-ribosylation factor 1, putative / 0.661
4ylg GDPADP-ribosylation factor 1, putative / 0.661
4bub ADPUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase / 0.660
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.659
4qos ADPPsp operon transcriptional activator / 0.659
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.658
3k9l GNPGTPase HRas / 0.658
4dsn GCPGTPase KRas / 0.658
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.656
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
3pcr GTPADP-ribosylation factor 6 / 0.656
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.655
3kz1 GSPTransforming protein RhoA / 0.655
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.653
1zc4 GNPRas-related protein Ral-A / 0.652
4oi2 ADPProtein clpf-1 / 0.652
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.651
4iei ADPGene 2 protein / 0.651
2vf7 ADPUvrABC system protein A / 0.650
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.650