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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
3pyz ANP Dihydrofolate synthase/folylpolyglutamate synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 1.129
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 1.069
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.975
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.844
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.830
2vor ACPFolylpolyglutamate synthase / 0.815
2vos ADPFolylpolyglutamate synthase / 0.771
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.750
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.741
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.741
1p3j AP5Adenylate kinase / 0.738
1kmq GNPTransforming protein RhoA / 0.731
1rrg GDPADP-ribosylation factor 1 / 0.731
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.730
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.726
1ow3 GDPTransforming protein RhoA / 0.725
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.724
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.724
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.716
3rab GNPRas-related protein Rab-3A / 0.716
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.715
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.714
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.714
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.714
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.714
3i3s GNPGTPase HRas / 0.714
1svl ADPLarge T antigen 3.6.4 0.713
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.712
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.712
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.712
3rsl GNPGTPase HRas / 0.712
4js0 GNPCell division control protein 42 homolog / 0.711
1m7b GTPRho-related GTP-binding protein RhoE / 0.710
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.710
1z2a GDPRas-related protein Rab-23 / 0.710
2c5l GTPGTPase HRas / 0.710
2j5x GSPADP-ribosylation factor 6 / 0.710
2rge GNPGTPase HRas / 0.710
3k8y GNPGTPase HRas / 0.710
3zfd ANPChromosome-associated kinesin KIF4 / 0.710
4l9w GNPGTPase HRas / 0.710
1t91 GTPRas-related protein Rab-7a / 0.709
2bme GNPRas-related protein Rab-4A / 0.709
1n6l GTPRas-related protein Rab-5A / 0.708
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.708
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
1yu9 GNPRas-related protein Rab-4A / 0.708
3oiw GNPGTPase HRas / 0.708
3rs0 GNPGTPase HRas / 0.708
3zia ATPATP synthase subunit alpha, mitochondrial / 0.708
4dls GNPGTPase HRas / 0.708
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.708
4rkf GNPRas-related protein Rab-3 / 0.708
4db1 ANPMyosin-7 / 0.707
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.706
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.706
1z2c GNPRho-related GTP-binding protein RhoC / 0.705
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.705
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.705
3kuc GDPRas-related protein Rap-1A / 0.705
3tlx ADPAdenylate kinase 2 / 0.705
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.705
1svm ATPLarge T antigen 3.6.4 0.704
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.704
3l8y GNPGTPase HRas / 0.704
3oiv GNPGTPase HRas / 0.704
3qbt GNPRas-related protein Rab-8A / 0.704
3tjz GNPADP-ribosylation factor 1 / 0.704
2bc9 GNPGuanylate-binding protein 1 / 0.703
4qbg AP5Adenylate kinase / 0.703
4ql3 GDPGTPase KRas / 0.703
5jlj GNPGTP-binding nuclear protein Ran / 0.703
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.701
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.700
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.699
4jjz ADPFormate--tetrahydrofolate ligase / 0.699
2pg2 ADPKinesin-like protein KIF11 / 0.696
3cob ADPKinesin heavy chain-like protein / 0.696
2x7e ADPKinesin-like protein KIF11 / 0.695
4cf7 ADPAdenylate kinase / 0.695
4lhw GNPRas-related protein Rab-8A / 0.695
4y0v GDPADP-ribosylation factor 1, putative / 0.695
4ylg GDPADP-ribosylation factor 1, putative / 0.695
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.694
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.694
1oix GDPRas-related protein Rab-11A / 0.694
2uyi ADPKinesin-like protein KIF11 / 0.694
3ddc GNPGTPase HRas / 0.694
3oiu GNPGTPase HRas / 0.694
3v4f GNPGTPase HRas / 0.694
4luc GDPGTPase KRas / 0.693
1mmg AGSMyosin-2 heavy chain / 0.692
3lbn GNPGTPase HRas / 0.692
3x1w GDPRas-related protein Rap-1b / 0.692
4goj GNPADP-ribosylation factor-like protein 3 / 0.692
4hdo GNPRas-related protein Rap-1b / 0.692
4ihq ADPConserved Archaeal protein / 0.692
4lv6 GDPGTPase KRas / 0.692
4tq9 GDPGTPase KRas / 0.692
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.691
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.691
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.691
2y65 ADPKinesin heavy chain / 0.691
3mjh GTPRas-related protein Rab-5A / 0.691
1xtr GNPGTP-binding protein Rheb / 0.690
4dso GSPGTPase KRas / 0.690
4nh0 ATPESX secretion system protein EccC / 0.690
1sdm ADPKinesin heavy chain-like protein / 0.689
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.689
2rgc GNPGTPase HRas / 0.689
3rs4 GNPGTPase HRas / 0.689
3rs5 GNPGTPase HRas / 0.689
1cxz GSPTransforming protein RhoA / 0.688
1ky2 GNPGTP-binding protein YPT7 / 0.688
3kud GDPGTPase HRas / 0.688
3x1z GNPRas-related protein Rap-1b / 0.688
4l8g GDPGTPase KRas / 0.688
4obe GDPGTPase KRas / 0.687
5dif GNPGTP-binding nuclear protein Ran / 0.687
1w5t ANPORC1-type DNA replication protein 2 / 0.685
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.684
4asu ADPATP synthase subunit alpha, mitochondrial / 0.684
4hdq GNPRas-related protein Rap-1b / 0.684
4jlo ADPAdenylate kinase / 0.684
1k5d GNPGTP-binding nuclear protein Ran / 0.683
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.683
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.683
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.683
3ref GDPRho family GTPase / 0.682
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.682
3w3z GTPGTP-binding nuclear protein Ran / 0.682
1ank ANPAdenylate kinase / 0.681
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
2dpx GDPGTP-binding protein RAD / 0.681
3oee ANPATP synthase subunit alpha, mitochondrial / 0.681
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
4jsy GTPMetallophosphoesterase / 0.681
3sop GDPNeuronal-specific septin-3 / 0.680
4o2l GTPGTP-binding protein Rheb / 0.680
4yqf GDPSeptin-9 / 0.680
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.679
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.679
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.679
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.678
4nl4 ADPPrimosomal protein N' / 0.678
4uj3 GNPRas-related protein Rab-11A / 0.678
1f5n GNPGuanylate-binding protein 1 / 0.677
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.677
2rgg GNPGTPase HRas / 0.677
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.677
3k1j ADPATP-dependent protease Lon / 0.677
3myk ANPMyosin-2 heavy chain / 0.677
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.677
1s1c GNPTransforming protein RhoA / 0.676
1vg8 GNPRas-related protein Rab-7a / 0.676
3ftq GNPSeptin-2 / 0.676
2rgb GNPGTPase HRas / 0.675
3tqc ADPPantothenate kinase / 0.675
4dlt GNPGTPase HRas / 0.675
4dlw GNPGTPase HRas / 0.675
1fmw ATPMyosin-2 heavy chain / 0.674
3b1x GNPFerrous iron transport protein B / 0.674
3q9l ATPSeptum site-determining protein MinD / 0.674
3rs7 GNPGTPase HRas / 0.674
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.674
4kvg GTPRas-related protein Rap-1A / 0.674
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.674
3kko GNPRas-related protein M-Ras / 0.673
4dlx GNPGTPase HRas / 0.673
4dlz GNPGTPase HRas / 0.673
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.672
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
2o8b ADPDNA mismatch repair protein Msh2 / 0.672
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.672
3oes GNPGTPase RhebL1 / 0.672
4a1z ADPKinesin-like protein KIF11 / 0.672
4bub ADPUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase / 0.672
4idn GNPAtlastin-1 3.6.5 0.672
4nyj GNPGTPase HRas / 0.672
1yrs ADPKinesin-like protein KIF11 / 0.671
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.671
4dlv GNPGTPase HRas / 0.671
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.670
5cyo GDPSeptin-9 / 0.670
1w5t ADPORC1-type DNA replication protein 2 / 0.669
3tgp GNPGTPase HRas / 0.669
3vhx GTPADP-ribosylation factor 6 / 0.669
4epx GDPGTPase KRas / 0.669
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.668
2qen ADPWalker-Type ATPase / 0.668
2xae ADPKinesin-like protein KIF11 / 0.668
2q3f GNPRas-related GTP-binding protein D / 0.667
2zts ADPUncharacterized protein / 0.667
4cym GCPRas-related protein Rab-32 / 0.667
5dha GNPGTP-binding nuclear protein Ran / 0.667
2vp0 TTPDeoxynucleoside kinase / 0.666
3kz1 GSPTransforming protein RhoA / 0.666
2jlr ANPGenome polyprotein 3.4.21.91 0.665
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.665
3wyf GTPGTP-binding nuclear protein / 0.665
4hut ATPCob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 0.665
4mkh AP5Adenylate kinase / 0.665
1tu3 GNPRas-related protein Rab-5A / 0.664
5b2z GNPGTPase HRas / 0.663
1ii6 ADPKinesin-like protein KIF11 / 0.662
2bku GTPGTP-binding nuclear protein Ran / 0.662
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.662
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
3k9l GNPGTPase HRas / 0.662
2fg5 GNPRas-related protein Rab-31 / 0.661
3tso GNPRas-related protein Rab-25 / 0.661
4l9s GDPGTPase HRas / 0.661
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.660
1x1r GDPRas-related protein M-Ras / 0.660
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.659
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.659
1sq5 ADPPantothenate kinase 2.7.1.33 0.659
3kkq GDPRas-related protein M-Ras / 0.659
3nbx ADPATPase RavA 3.6.3 0.659
4a28 ADPKinesin-like protein KIF11 / 0.659
4epw GDPGTPase KRas / 0.659
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.658
1mma ADPMyosin-2 heavy chain / 0.658
3lbi GNPGTPase HRas / 0.658
2gcp GSPRho-related GTP-binding protein RhoC / 0.657
3q5d GDPAtlastin-1 3.6.5 0.657
4tyq AP5Adenylate kinase / 0.657
1a2b GSPTransforming protein RhoA / 0.656
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.655
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.655
4dsu GDPGTPase KRas / 0.655
4fg9 ATPCalcium/calmodulin-dependent protein kinase type 1 2.7.11.17 0.655
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.654
3law GNPRas-related protein Rab-7a / 0.654
3lbh GNPGTPase HRas / 0.654
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.654
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.654
4qxa GTPRas-related protein Rab-9A / 0.654
3eg5 GNPCell division control protein 42 homolog / 0.653
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.653
1lfd GNPGTPase HRas / 0.652
2ffq GSPRas-related protein Rab-6B / 0.652
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.652
1ibr GNPGTP-binding nuclear protein Ran / 0.651
1p9w ANPType II secretion system protein E / 0.651
4gp6 ADPMetallophosphoesterase / 0.651
5ftc ADPTPR domain protein / 0.651
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.650
3pcr GTPADP-ribosylation factor 6 / 0.650
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.650
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.650