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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
3qcz ANP Dihydrofolate synthase/folylpolyglutamate synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 1.149
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 1.069
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.949
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.899
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.896
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.840
2vor ACPFolylpolyglutamate synthase / 0.816
2vos ADPFolylpolyglutamate synthase / 0.792
2j5x GSPADP-ribosylation factor 6 / 0.746
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.745
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.743
4qbg AP5Adenylate kinase / 0.739
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.735
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.732
1rrg GDPADP-ribosylation factor 1 / 0.730
5ftc ADPTPR domain protein / 0.730
4jl5 ADPAdenylate kinase / 0.729
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.728
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.727
4db1 ANPMyosin-7 / 0.727
1ow3 GDPTransforming protein RhoA / 0.724
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.724
4g0n GNPGTPase HRas / 0.721
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.720
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.719
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.717
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.717
3oiu GNPGTPase HRas / 0.716
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.714
3oiw GNPGTPase HRas / 0.714
5b2z GNPGTPase HRas / 0.714
1mmg AGSMyosin-2 heavy chain / 0.713
1n6l GTPRas-related protein Rab-5A / 0.713
3ddc GNPGTPase HRas / 0.713
4jld ADPAdenylate kinase / 0.713
4jlo ADPAdenylate kinase / 0.713
4dlx GNPGTPase HRas / 0.711
4dso GSPGTPase KRas / 0.711
1kmq GNPTransforming protein RhoA / 0.710
1m7b GTPRho-related GTP-binding protein RhoE / 0.709
3rsl GNPGTPase HRas / 0.709
4dls GNPGTPase HRas / 0.709
4lhw GNPRas-related protein Rab-8A / 0.709
3tjz GNPADP-ribosylation factor 1 / 0.708
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.707
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.707
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.707
3w3z GTPGTP-binding nuclear protein Ran / 0.707
5dif GNPGTP-binding nuclear protein Ran / 0.707
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.706
1w5t ANPORC1-type DNA replication protein 2 / 0.706
1yu9 GNPRas-related protein Rab-4A / 0.706
2bme GNPRas-related protein Rab-4A / 0.706
2rgb GNPGTPase HRas / 0.706
1e4v AP5Adenylate kinase / 0.705
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.705
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.705
2y65 ADPKinesin heavy chain / 0.705
4ihq ADPConserved Archaeal protein / 0.705
5jlj GNPGTP-binding nuclear protein Ran / 0.705
2rgc GNPGTPase HRas / 0.704
4dlt GNPGTPase HRas / 0.704
4goj GNPADP-ribosylation factor-like protein 3 / 0.704
2q3f GNPRas-related GTP-binding protein D / 0.703
4jky ADPAdenylate kinase / 0.703
1rj9 GCPSignal recognition particle receptor FtsY / 0.702
4jjz ADPFormate--tetrahydrofolate ligase / 0.701
3l8y GNPGTPase HRas / 0.700
4dlv GNPGTPase HRas / 0.700
4nyj GNPGTPase HRas / 0.700
1z0d GDPRas-related protein Rab-5C / 0.699
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.699
4asu ADPATP synthase subunit alpha, mitochondrial / 0.699
4dlz GNPGTPase HRas / 0.699
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.698
3law GNPRas-related protein Rab-7a / 0.698
1sq5 ADPPantothenate kinase 2.7.1.33 0.697
4l9w GNPGTPase HRas / 0.696
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.696
4ylg GDPADP-ribosylation factor 1, putative / 0.696
1gwn GTPRho-related GTP-binding protein RhoE / 0.695
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.695
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.695
4hdo GNPRas-related protein Rap-1b / 0.695
4jl6 ADPAdenylate kinase / 0.695
4y0v GDPADP-ribosylation factor 1, putative / 0.695
1xtr GNPGTP-binding protein Rheb / 0.694
3lbh GNPGTPase HRas / 0.694
3lbn GNPGTPase HRas / 0.694
3oee ANPATP synthase subunit alpha, mitochondrial / 0.694
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.694
3ftq GNPSeptin-2 / 0.693
4ap0 ADPKinesin-like protein KIF11 / 0.693
4nh0 ATPESX secretion system protein EccC / 0.693
3kko GNPRas-related protein M-Ras / 0.692
4cf7 ADPAdenylate kinase / 0.692
4tyq AP5Adenylate kinase / 0.692
4xsg GSPTransforming protein RhoA / 0.692
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.691
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.690
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.690
1cxz GSPTransforming protein RhoA / 0.689
1xmv ADPProtein RecA / 0.689
1z0f GDPRas-related protein Rab-14 / 0.689
2fna ADPUncharacterized protein / 0.689
3kkq GDPRas-related protein M-Ras / 0.689
3tgp GNPGTPase HRas / 0.689
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.689
4xoi GTPTransforming protein RhoA / 0.689
4xvq GNPGTPase HRas / 0.689
1sdm ADPKinesin heavy chain-like protein / 0.688
4l8g GDPGTPase KRas / 0.688
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.688
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.687
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.687
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.687
3rs7 GNPGTPase HRas / 0.687
4l9s GDPGTPase HRas / 0.687
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.686
2rgg GNPGTPase HRas / 0.686
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.686
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.686
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.686
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.685
2xae ADPKinesin-like protein KIF11 / 0.685
2cl6 CAGGTPase HRas / 0.684
2dr3 ADPUPF0273 protein PH0284 / 0.684
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.684
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.684
3oes GNPGTPase RhebL1 / 0.684
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.684
4luc GDPGTPase KRas / 0.684
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.683
3cob ADPKinesin heavy chain-like protein / 0.683
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.682
1yrs ADPKinesin-like protein KIF11 / 0.682
3ref GDPRho family GTPase / 0.682
3vhx GTPADP-ribosylation factor 6 / 0.682
1uad GNPRas-related protein Ral-A / 0.681
4pk4 ADPUnconventional myosin-VI / 0.681
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.680
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.680
3b1x GNPFerrous iron transport protein B / 0.680
3kuc GDPRas-related protein Rap-1A / 0.680
1ake AP5Adenylate kinase / 0.679
3zfd ANPChromosome-associated kinesin KIF4 / 0.679
4dsn GCPGTPase KRas / 0.679
4nl4 ADPPrimosomal protein N' / 0.679
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.678
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.678
3sop GDPNeuronal-specific septin-3 / 0.678
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.678
4js0 GNPCell division control protein 42 homolog / 0.678
1t91 GTPRas-related protein Rab-7a / 0.677
1x1r GDPRas-related protein M-Ras / 0.677
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.677
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.677
2o8b ADPDNA mismatch repair protein Msh2 / 0.676
4qxa GTPRas-related protein Rab-9A / 0.676
1p9w ANPType II secretion system protein E / 0.675
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.675
2rge GNPGTPase HRas / 0.675
3k8y GNPGTPase HRas / 0.675
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.675
1z2a GDPRas-related protein Rab-23 / 0.674
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.673
2bku GTPGTP-binding nuclear protein Ran / 0.673
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.673
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.673
1tu3 GNPRas-related protein Rab-5A / 0.672
1zbd GTPRas-related protein Rab-3A / 0.672
3tso GNPRas-related protein Rab-25 / 0.672
4idn GNPAtlastin-1 3.6.5 0.672
4qos ADPPsp operon transcriptional activator / 0.672
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.671
3hqd ANPKinesin-like protein KIF11 / 0.671
1ky2 GNPGTP-binding protein YPT7 / 0.670
2fg5 GNPRas-related protein Rab-31 / 0.670
3mjh GTPRas-related protein Rab-5A / 0.670
3rab GNPRas-related protein Rab-3A / 0.670
3x1w GDPRas-related protein Rap-1b / 0.670
3x1z GNPRas-related protein Rap-1b / 0.670
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.669
1xts GTPGTP-binding protein Rheb / 0.669
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.669
1wbb ADPDNA mismatch repair protein MutS / 0.668
1yzq GNPRas-related protein Rab-6A / 0.668
2uyi ADPKinesin-like protein KIF11 / 0.668
4bub ADPUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase / 0.668
4lv6 GDPGTPase KRas / 0.668
1svl ADPLarge T antigen 3.6.4 0.667
4dlw GNPGTPase HRas / 0.667
1ank ANPAdenylate kinase / 0.666
2gcp GSPRho-related GTP-binding protein RhoC / 0.665
2ql6 ADPNicotinamide riboside kinase 1 / 0.665
3tqc ADPPantothenate kinase / 0.665
3v4f GNPGTPase HRas / 0.665
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
4gp6 ADPMetallophosphoesterase / 0.665
4hut ATPCob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 0.665
5aun ADPIron-sulfur cluster carrier protein / 0.665
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.664
1mma ADPMyosin-2 heavy chain / 0.664
1xms ANPProtein RecA / 0.664
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.664
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.664
3rs0 GNPGTPase HRas / 0.664
3rs4 GNPGTPase HRas / 0.664
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.664
4oi2 ADPProtein clpf-1 / 0.664
1esn ANPPantothenate kinase 2.7.1.33 0.663
1s1c GNPTransforming protein RhoA / 0.663
1ibr GNPGTP-binding nuclear protein Ran / 0.662
2ce2 GDPGTPase HRas / 0.662
2pg2 ADPKinesin-like protein KIF11 / 0.662
1g17 GNPRas-related protein SEC4 / 0.661
2gil GTPRas-related protein Rab-6A / 0.661
2gm1 ADPKinesin-like protein KIF11 / 0.661
2vf7 ADPUvrABC system protein A / 0.661
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.661
1k5d GNPGTP-binding nuclear protein Ran / 0.660
1zc3 GNPRas-related protein Ral-A / 0.660
1am4 GNPCell division control protein 42 homolog / 0.659
1ii6 ADPKinesin-like protein KIF11 / 0.658
1zc4 GNPRas-related protein Ral-A / 0.658
2hld ANPATP synthase subunit alpha, mitochondrial / 0.658
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.658
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
3eg5 GNPCell division control protein 42 homolog / 0.658
3kud GDPGTPase HRas / 0.658
4obe GDPGTPase KRas / 0.658
3qtt ANPPantothenate synthetase / 0.657
4pjk ADPMyosin-2 heavy chain / 0.657
4xr9 TMPCalS8 / 0.657
1z2c GNPRho-related GTP-binding protein RhoC / 0.656
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.656
3oiv GNPGTPase HRas / 0.656
3rs5 GNPGTPase HRas / 0.656
1a2b GSPTransforming protein RhoA / 0.655
1w5s ADPORC1-type DNA replication protein 2 / 0.655
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.655
3tkl GTPRas-related protein Rab-1A / 0.655
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.655
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.654
3pit GNPRas-related protein M-Ras / 0.654
4a1z ADPKinesin-like protein KIF11 / 0.654
1z0a GDPRas-related protein Rab-2A / 0.653
4idp GNPAtlastin-1 3.6.5 0.653
4rkf GNPRas-related protein Rab-3 / 0.653
4z54 GDPNeuronal-specific septin-3 / 0.653
1oix GDPRas-related protein Rab-11A / 0.652
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.652
2dpx GDPGTP-binding protein RAD / 0.652
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.650
4cym GCPRas-related protein Rab-32 / 0.650
4fdp FADDecaprenylphosphoryl-beta-D-ribose oxidase / 0.650