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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
1w7k ADP Dihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 1.137
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.975
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.949
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.849
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.847
2vos ADPFolylpolyglutamate synthase / 0.780
2vor ACPFolylpolyglutamate synthase / 0.776
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.770
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.754
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.754
2j5x GSPADP-ribosylation factor 6 / 0.744
3pit GNPRas-related protein M-Ras / 0.737
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.736
1rrg GDPADP-ribosylation factor 1 / 0.731
3l8y GNPGTPase HRas / 0.728
2rgb GNPGTPase HRas / 0.724
4l9w GNPGTPase HRas / 0.724
3lbh GNPGTPase HRas / 0.723
3lbn GNPGTPase HRas / 0.723
3oiu GNPGTPase HRas / 0.723
4dlv GNPGTPase HRas / 0.723
3rs7 GNPGTPase HRas / 0.722
4dlw GNPGTPase HRas / 0.722
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.721
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.721
3kuc GDPRas-related protein Rap-1A / 0.721
4dlx GNPGTPase HRas / 0.721
4jsy GTPMetallophosphoesterase / 0.721
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.720
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.720
1z0d GDPRas-related protein Rab-5C / 0.719
3tlx ADPAdenylate kinase 2 / 0.719
4g0n GNPGTPase HRas / 0.719
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.718
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.718
4dls GNPGTPase HRas / 0.718
4gp6 ADPMetallophosphoesterase / 0.718
4lhw GNPRas-related protein Rab-8A / 0.718
3law GNPRas-related protein Rab-7a / 0.716
5jlj GNPGTP-binding nuclear protein Ran / 0.716
1rj9 GCPSignal recognition particle receptor FtsY / 0.715
4cf7 ADPAdenylate kinase / 0.714
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.711
3rab GNPRas-related protein Rab-3A / 0.711
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.710
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
3rs0 GNPGTPase HRas / 0.710
3rsl GNPGTPase HRas / 0.710
3v4f GNPGTPase HRas / 0.710
4dlt GNPGTPase HRas / 0.710
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.709
2rgc GNPGTPase HRas / 0.709
3k8y GNPGTPase HRas / 0.709
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.709
4dlz GNPGTPase HRas / 0.709
4rkf GNPRas-related protein Rab-3 / 0.709
5b2z GNPGTPase HRas / 0.709
1oix GDPRas-related protein Rab-11A / 0.708
3oiw GNPGTPase HRas / 0.708
4asu ADPATP synthase subunit alpha, mitochondrial / 0.708
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.708
1z2a GDPRas-related protein Rab-23 / 0.707
3lbi GNPGTPase HRas / 0.707
3x1z GNPRas-related protein Rap-1b / 0.707
1d5c GDPGTPase (Rab6) / 0.706
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.706
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.706
4ihq ADPConserved Archaeal protein / 0.706
4q03 GDPGTPase KRas / 0.706
2rge GNPGTPase HRas / 0.705
3ddc GNPGTPase HRas / 0.705
1yu9 GNPRas-related protein Rab-4A / 0.704
2y65 ADPKinesin heavy chain / 0.704
4nyj GNPGTPase HRas / 0.704
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.703
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.703
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.703
4hdo GNPRas-related protein Rap-1b / 0.703
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.701
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.701
2rgx AP5Adenylate kinase / 0.701
1zc4 GNPRas-related protein Ral-A / 0.700
2bc9 GNPGuanylate-binding protein 1 / 0.700
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.700
1ii6 ADPKinesin-like protein KIF11 / 0.699
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.699
3oiv GNPGTPase HRas / 0.699
3rs5 GNPGTPase HRas / 0.699
3zfd ANPChromosome-associated kinesin KIF4 / 0.699
4xvq GNPGTPase HRas / 0.699
3rs4 GNPGTPase HRas / 0.698
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.697
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.697
4qxa GTPRas-related protein Rab-9A / 0.697
1m7b GTPRho-related GTP-binding protein RhoE / 0.696
2bme GNPRas-related protein Rab-4A / 0.696
4xoi GTPTransforming protein RhoA / 0.696
4yqf GDPSeptin-9 / 0.696
1svm ATPLarge T antigen 3.6.4 0.695
1xtr GNPGTP-binding protein Rheb / 0.695
2x7e ADPKinesin-like protein KIF11 / 0.695
4ylg GDPADP-ribosylation factor 1, putative / 0.695
1z2c GNPRho-related GTP-binding protein RhoC / 0.694
2bku GTPGTP-binding nuclear protein Ran / 0.694
2gcp GSPRho-related GTP-binding protein RhoC / 0.694
4y0v GDPADP-ribosylation factor 1, putative / 0.694
1f5n GNPGuanylate-binding protein 1 / 0.693
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.693
1p9w ANPType II secretion system protein E / 0.693
1x1r GDPRas-related protein M-Ras / 0.693
2uyi ADPKinesin-like protein KIF11 / 0.693
4jl6 ADPAdenylate kinase / 0.693
4l8g GDPGTPase KRas / 0.693
5di3 GNPADP-ribosylation factor-like protein 3 / 0.693
2x2r ADPKinesin-like protein KIF11 / 0.692
4jlo ADPAdenylate kinase / 0.692
4l9s GDPGTPase HRas / 0.692
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.692
5aun ADPIron-sulfur cluster carrier protein / 0.692
1kmq GNPTransforming protein RhoA / 0.691
3x1w GDPRas-related protein Rap-1b / 0.691
4luc GDPGTPase KRas / 0.691
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.691
4epw GDPGTPase KRas / 0.690
1mmg AGSMyosin-2 heavy chain / 0.689
1ow3 GDPTransforming protein RhoA / 0.689
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.689
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
2dpx GDPGTP-binding protein RAD / 0.689
3kko GNPRas-related protein M-Ras / 0.689
4ap0 ADPKinesin-like protein KIF11 / 0.689
1ake AP5Adenylate kinase / 0.688
1cxz GSPTransforming protein RhoA / 0.688
1esn ANPPantothenate kinase 2.7.1.33 0.688
2rgg GNPGTPase HRas / 0.688
3mjh GTPRas-related protein Rab-5A / 0.687
4db1 ANPMyosin-7 / 0.687
4nl4 ADPPrimosomal protein N' / 0.686
3ref GDPRho family GTPase / 0.685
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.685
4z54 GDPNeuronal-specific septin-3 / 0.685
1sq5 ADPPantothenate kinase 2.7.1.33 0.684
1vg8 GNPRas-related protein Rab-7a / 0.684
3qbt GNPRas-related protein Rab-8A / 0.684
3zia ATPATP synthase subunit alpha, mitochondrial / 0.684
4dxa GSPRas-related protein Rap-1b / 0.684
2q2y ADPKinesin-like protein KIF11 / 0.683
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.683
3i3s GNPGTPase HRas / 0.683
3tso GNPRas-related protein Rab-25 / 0.683
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.682
4hdq GNPRas-related protein Rap-1b / 0.682
4nh0 ATPESX secretion system protein EccC / 0.682
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.682
4tq9 GDPGTPase KRas / 0.682
4ys0 ADPProtein translocase subunit SecA / 0.682
4dso GSPGTPase KRas / 0.681
4epx GDPGTPase KRas / 0.681
4xvu ATPATPase GET3 / 0.681
2eck ADPAdenylate kinase / 0.680
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.680
3sop GDPNeuronal-specific septin-3 / 0.680
2vf7 ADPUvrABC system protein A / 0.679
3r9i ADPSeptum site-determining protein MinD / 0.679
4o2r GDPGTP-binding protein Rheb / 0.679
1ky2 GNPGTP-binding protein YPT7 / 0.678
2q3f GNPRas-related GTP-binding protein D / 0.678
3w3z GTPGTP-binding nuclear protein Ran / 0.678
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.678
1yzq GNPRas-related protein Rab-6A / 0.677
3b1x GNPFerrous iron transport protein B / 0.677
4dsn GCPGTPase KRas / 0.677
4js0 GNPCell division control protein 42 homolog / 0.677
3vhx GTPADP-ribosylation factor 6 / 0.676
4hut ATPCob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 0.676
1s1c GNPTransforming protein RhoA / 0.675
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.675
2fg5 GNPRas-related protein Rab-31 / 0.675
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.675
5dha GNPGTP-binding nuclear protein Ran / 0.674
1ank ANPAdenylate kinase / 0.672
4cym GCPRas-related protein Rab-32 / 0.672
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.671
3a58 GNPGTP-binding protein RHO1 / 0.671
3ftq GNPSeptin-2 / 0.670
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.669
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.669
1w5t ANPORC1-type DNA replication protein 2 / 0.667
2l0x GDPGTP-binding protein Rheb / 0.667
2o8b ADPDNA mismatch repair protein Msh2 / 0.667
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.666
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.666
4jky ADPAdenylate kinase / 0.666
5k5z ANPUncharacterized protein / 0.666
1mma ADPMyosin-2 heavy chain / 0.665
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.664
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.664
3bxz ADPProtein translocase subunit SecA / 0.664
4pk4 ADPUnconventional myosin-VI / 0.664
1svl ADPLarge T antigen 3.6.4 0.663
3oee ANPATP synthase subunit alpha, mitochondrial / 0.663
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
4a28 ADPKinesin-like protein KIF11 / 0.662
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.661
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.660
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.660
1xts GTPGTP-binding protein Rheb / 0.660
1z0a GDPRas-related protein Rab-2A / 0.660
2hld ANPATP synthase subunit alpha, mitochondrial / 0.660
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
4a1z ADPKinesin-like protein KIF11 / 0.660
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.659
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.658
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.658
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.658
4wa7 GDPGTPase KRas / 0.658
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.657
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.657
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.657
4qos ADPPsp operon transcriptional activator / 0.657
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.656
3k3b ADPKinesin-like protein KIF11 / 0.656
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.656
5c46 GSPRas-related protein Rab-11A / 0.656
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.655
4dsu GDPGTPase KRas / 0.655
4uj5 GNPRas-related protein Rab-11A / 0.655
1xmv ADPProtein RecA / 0.653
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.652
4o2l GTPGTP-binding protein Rheb / 0.651
1ibr GNPGTP-binding nuclear protein Ran / 0.650
1z0f GDPRas-related protein Rab-14 / 0.650
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.650
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.650