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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
2fgk ATP Alpha-hemolysin translocation ATP-binding protein HlyB

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 1.133
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 1.049
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.999
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.962
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.889
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.842
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.827
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.827
4qm6 GTPMetallophosphoesterase / 0.821
1t91 GTPRas-related protein Rab-7a / 0.812
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.807
1wa5 GTPGTP-binding nuclear protein Ran / 0.802
3myk ANPMyosin-2 heavy chain / 0.792
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.791
3rab GNPRas-related protein Rab-3A / 0.790
5dha GNPGTP-binding nuclear protein Ran / 0.787
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.778
4c2u ANPDNA helicase / 0.778
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.777
1wdt GTPElongation factor G (EF-G-2) / 0.776
3c41 ANPAmino acid ABC transporter / 0.776
3mjh GTPRas-related protein Rab-5A / 0.776
1fmw ATPMyosin-2 heavy chain / 0.775
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.775
4dso GSPGTPase KRas / 0.774
1yu9 GNPRas-related protein Rab-4A / 0.772
3vhx GTPADP-ribosylation factor 6 / 0.769
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.768
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.766
1m7b GTPRho-related GTP-binding protein RhoE / 0.765
4k81 GTPGTPase HRas / 0.765
1cxz GSPTransforming protein RhoA / 0.763
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.760
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.759
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.752
2r6g ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.750
1mmg AGSMyosin-2 heavy chain / 0.749
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.748
4ol0 GTPGTP-binding nuclear protein Ran / 0.748
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.748
2vf7 ADPUvrABC system protein A / 0.747
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.744
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.744
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.743
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.743
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.742
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.742
1gwn GTPRho-related GTP-binding protein RhoE / 0.739
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.739
3w3z GTPGTP-binding nuclear protein Ran / 0.738
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.738
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.737
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.736
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.736
4cym GCPRas-related protein Rab-32 / 0.735
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.734
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.732
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.731
2ffq GSPRas-related protein Rab-6B / 0.728
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.727
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.727
4xoi GTPTransforming protein RhoA / 0.726
2dpx GDPGTP-binding protein RAD / 0.723
1mma ADPMyosin-2 heavy chain / 0.721
2gil GTPRas-related protein Rab-6A / 0.721
1yra GDPGPN-loop GTPase PAB0955 / 0.720
4mkh AP5Adenylate kinase / 0.720
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.715
1z2c GNPRho-related GTP-binding protein RhoC / 0.715
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.714
4v02 ATPSite-determining protein / 0.714
4i1v ADPDephospho-CoA kinase / 0.713
1zio AP5Adenylate kinase / 0.712
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.712
1xmv ADPProtein RecA / 0.711
1wbb ADPDNA mismatch repair protein MutS / 0.710
5da9 AGSUncharacterized protein / 0.710
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.709
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.709
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.709
4b7b ADPKinesin-like protein KIF11 / 0.708
4lhv GDPRas-related protein Rab-8A / 0.706
2c5l GTPGTPase HRas / 0.705
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.705
1zbd GTPRas-related protein Rab-3A / 0.704
5di3 GNPADP-ribosylation factor-like protein 3 / 0.704
1yzq GNPRas-related protein Rab-6A / 0.703
2rgx AP5Adenylate kinase / 0.703
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.703
1sq5 ADPPantothenate kinase 2.7.1.33 0.702
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.702
4js0 GNPCell division control protein 42 homolog / 0.701
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.700
1s1c GNPTransforming protein RhoA / 0.700
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.699
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.699
2hld ANPATP synthase subunit alpha, mitochondrial / 0.696
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.696
5bn3 ADPV-type ATP synthase alpha chain / 0.695
5bn3 ADPNEQ263 / 0.695
2bc9 GNPGuanylate-binding protein 1 / 0.694
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.693
4lpk GDPGTPase KRas / 0.693
2q3f GNPRas-related GTP-binding protein D / 0.692
3hpr AP5Adenylate kinase / 0.691
3oiu GNPGTPase HRas / 0.691
4lrw GDPGTPase KRas / 0.691
3oee ANPATP synthase subunit alpha, mitochondrial / 0.690
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
4a1z ADPKinesin-like protein KIF11 / 0.690
2bme GNPRas-related protein Rab-4A / 0.688
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.687
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.687
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.687
2zr9 DTPProtein RecA / 0.687
4dls GNPGTPase HRas / 0.687
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.686
4uj5 GNPRas-related protein Rab-11A / 0.686
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.685
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.685
5dac AGSUncharacterized protein / 0.685
1vg8 GNPRas-related protein Rab-7a / 0.682
4o3m ADPBloom syndrome protein 3.6.4.12 0.681
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.679
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.679
3oiw GNPGTPase HRas / 0.679
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.679
3pcr GTPADP-ribosylation factor 6 / 0.678
4kvg GTPRas-related protein Rap-1A / 0.678
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.678
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.678
1mab ATPATP synthase subunit alpha, mitochondrial / 0.677
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.676
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.676
3a58 GNPGTP-binding protein RHO1 / 0.676
3tjz GNPADP-ribosylation factor 1 / 0.676
2zsb ADPPantothenate kinase 2.7.1.33 0.675
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.674
1svl ADPLarge T antigen 3.6.4 0.674
1k5d GNPGTP-binding nuclear protein Ran / 0.673
3e5h GNPRas-related protein Rab-28 / 0.673
4jsy GTPMetallophosphoesterase / 0.673
2bbw GP5Adenylate kinase 4, mitochondrial / 0.670
3i3s GNPGTPase HRas / 0.670
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.669
4dlv GNPGTPase HRas / 0.668
4zca ADPKinesin-like protein KIF11 / 0.668
3bc1 GNPRas-related protein Rab-27A / 0.667
3rs5 GNPGTPase HRas / 0.667
4hdo GNPRas-related protein Rap-1b / 0.667
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.666
4m2b UPGUDP-glucose pyrophosphorylase / 0.666
2r9v ATPATP synthase subunit alpha / 0.665
2zs9 ADPPantothenate kinase 2.7.1.33 0.665
4qos ADPPsp operon transcriptional activator / 0.664
4uj3 GNPRas-related protein Rab-11A / 0.664
1kmq GNPTransforming protein RhoA / 0.663
1tu3 GNPRas-related protein Rab-5A / 0.663
3nbx ADPATPase RavA 3.6.3 0.663
5k5z ANPUncharacterized protein / 0.663
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.663
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.662
1xts GTPGTP-binding protein Rheb / 0.662
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.660
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
2zrf DTPProtein RecA / 0.660
4rkf GNPRas-related protein Rab-3 / 0.660
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.659
3lbh GNPGTPase HRas / 0.659
3b1x GNPFerrous iron transport protein B / 0.658
1d5c GDPGTPase (Rab6) / 0.657
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.657
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.657
2dr3 ADPUPF0273 protein PH0284 / 0.657
4mit GTPRho-related protein racC / 0.657
1ii6 ADPKinesin-like protein KIF11 / 0.656
1xp8 AGSProtein RecA / 0.656
4l9w GNPGTPase HRas / 0.655
3bbp GTPRas-related protein Rab-6A / 0.654
1ny5 ADPTranscriptional regulator (NtrC family) / 0.653
2c96 ATPPsp operon transcriptional activator / 0.653
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.653
1zc3 GNPRas-related protein Ral-A / 0.652
2p5y NADUDP-glucose 4-epimerase / 0.650
5lc1 NADL-threonine 3-dehydrogenase / 0.650