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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
2c96 ATP Psp operon transcriptional activator

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2c96 ATPPsp operon transcriptional activator / 1.091
2c9c ATPPsp operon transcriptional activator / 0.905
4qnr ATPPsp operon transcriptional activator / 0.888
3m0e ATPTranscriptional regulator (NtrC family) / 0.851
4qos ADPPsp operon transcriptional activator / 0.822
4g0n GNPGTPase HRas / 0.790
5aun ADPIron-sulfur cluster carrier protein / 0.790
1a2b GSPTransforming protein RhoA / 0.778
1gwn GTPRho-related GTP-binding protein RhoE / 0.771
4o2l GTPGTP-binding protein Rheb / 0.771
3w3z GTPGTP-binding nuclear protein Ran / 0.769
4ww4 ADPRuvB-like helicase / 0.769
2bku GTPGTP-binding nuclear protein Ran / 0.767
4k81 GTPGTPase HRas / 0.767
4jsy GTPMetallophosphoesterase / 0.765
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.765
1z2c GNPRho-related GTP-binding protein RhoC / 0.764
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.763
4o25 GTPGTP-binding protein Rheb / 0.763
3a58 GNPGTP-binding protein RHO1 / 0.762
2ffq GSPRas-related protein Rab-6B / 0.761
3b1x GNPFerrous iron transport protein B / 0.761
1f5n GNPGuanylate-binding protein 1 / 0.760
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.760
3kz1 GSPTransforming protein RhoA / 0.760
5ftc ADPTPR domain protein / 0.760
4qxa GTPRas-related protein Rab-9A / 0.759
1cxz GSPTransforming protein RhoA / 0.758
4xoi GTPTransforming protein RhoA / 0.758
1e4v AP5Adenylate kinase / 0.757
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.757
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.757
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.757
2x2r ADPKinesin-like protein KIF11 / 0.756
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.756
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.755
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.755
4dvg GSPRho family GTPase / 0.754
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.754
4qm6 GTPMetallophosphoesterase / 0.753
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.753
1ake AP5Adenylate kinase / 0.752
1m7b GTPRho-related GTP-binding protein RhoE / 0.752
5c46 GSPRas-related protein Rab-11A / 0.752
1tu3 GNPRas-related protein Rab-5A / 0.751
3d8b ADPFidgetin-like protein 1 3.6.4 0.751
3tkl GTPRas-related protein Rab-1A / 0.751
4lhv GDPRas-related protein Rab-8A / 0.751
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.750
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.750
2pg2 ADPKinesin-like protein KIF11 / 0.748
2x7e ADPKinesin-like protein KIF11 / 0.748
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.747
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.747
2uyi ADPKinesin-like protein KIF11 / 0.746
2gcp GSPRho-related GTP-binding protein RhoC / 0.745
3tnf GNPRas-related protein Rab-8A / 0.745
3qbt GNPRas-related protein Rab-8A / 0.744
1n6l GTPRas-related protein Rab-5A / 0.743
3bc1 GNPRas-related protein Rab-27A / 0.742
2c5l GTPGTPase HRas / 0.741
1w5t ANPORC1-type DNA replication protein 2 / 0.740
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.739
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.738
2cl6 CAGGTPase HRas / 0.738
4xsg GSPTransforming protein RhoA / 0.738
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.737
2gil GTPRas-related protein Rab-6A / 0.736
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.735
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.735
4d81 ADPAAA ATPase, central domain protein / 0.735
1mmg AGSMyosin-2 heavy chain / 0.734
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.734
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.734
1wa5 GTPGTP-binding nuclear protein Ran / 0.733
4kvg GTPRas-related protein Rap-1A / 0.733
5dha GNPGTP-binding nuclear protein Ran / 0.733
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.732
1fnn ADPORC1-type DNA replication protein / 0.732
4idn GNPAtlastin-1 3.6.5 0.731
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.730
1xts GTPGTP-binding protein Rheb / 0.729
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.729
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.728
1zbd GTPRas-related protein Rab-3A / 0.728
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.727
3a6p GTPGTP-binding nuclear protein Ran / 0.727
1vg8 GNPRas-related protein Rab-7a / 0.725
1z2a GDPRas-related protein Rab-23 / 0.725
2ce2 GDPGTPase HRas / 0.725
3oes GNPGTPase RhebL1 / 0.725
4ldj GDPGTPase KRas / 0.725
4q03 GDPGTPase KRas / 0.725
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.725
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.724
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.724
5dif GNPGTP-binding nuclear protein Ran / 0.724
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.723
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.723
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.723
1zio AP5Adenylate kinase / 0.722
3ftq GNPSeptin-2 / 0.722
4l9w GNPGTPase HRas / 0.722
2gm1 ADPKinesin-like protein KIF11 / 0.721
2hld ANPATP synthase subunit alpha, mitochondrial / 0.721
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.721
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.721
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.721
2rgx AP5Adenylate kinase / 0.721
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.721
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.720
4idp GNPAtlastin-1 3.6.5 0.720
4ncl GDPEukaryotic translation initiation factor 5B / 0.720
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.719
1xtr GNPGTP-binding protein Rheb / 0.719
2xae ADPKinesin-like protein KIF11 / 0.719
3wyf GTPGTP-binding nuclear protein / 0.719
4lhw GNPRas-related protein Rab-8A / 0.719
3e5h GNPRas-related protein Rab-28 / 0.718
3mjh GTPRas-related protein Rab-5A / 0.718
3nbx ADPATPase RavA 3.6.3 0.718
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.718
4nh0 ATPESX secretion system protein EccC / 0.718
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.718
3rab GNPRas-related protein Rab-3A / 0.717
4asu ADPATP synthase subunit alpha, mitochondrial / 0.717
4dsu GDPGTPase KRas / 0.717
2bc9 GNPGuanylate-binding protein 1 / 0.716
3k1j ADPATP-dependent protease Lon / 0.716
1zc4 GNPRas-related protein Ral-A / 0.715
2fe4 GDPRas-related protein Rab-6B / 0.715
3myk ANPMyosin-2 heavy chain / 0.715
4mit GTPRho-related protein racC / 0.715
3zia ATPATP synthase subunit alpha, mitochondrial / 0.714
1fmw ATPMyosin-2 heavy chain / 0.713
4l8g GDPGTPase KRas / 0.713
5k5z ANPUncharacterized protein / 0.713
1lfd GNPGTPase HRas / 0.712
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.712
2xsz ATPRuvB-like 2 3.6.4.12 0.712
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.711
1d5c GDPGTPase (Rab6) / 0.710
1mab ATPATP synthase subunit alpha, mitochondrial / 0.710
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.710
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
1t91 GTPRas-related protein Rab-7a / 0.709
2dpx GDPGTP-binding protein RAD / 0.709
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.709
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.709
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.708
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.707
1ibr GNPGTP-binding nuclear protein Ran / 0.707
3cph GDPRas-related protein SEC4 / 0.707
4lrw GDPGTPase KRas / 0.707
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.706
2rgb GNPGTPase HRas / 0.706
3kud GDPGTPase HRas / 0.706
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.706
2r9v ATPATP synthase subunit alpha / 0.705
4v02 ATPSite-determining protein / 0.705
1mma ADPMyosin-2 heavy chain / 0.704
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.704
1s1c GNPTransforming protein RhoA / 0.704
2bbw GP5Adenylate kinase 4, mitochondrial / 0.704
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.704
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.704
1g17 GNPRas-related protein SEC4 / 0.703
1kmq GNPTransforming protein RhoA / 0.703
3q5d GDPAtlastin-1 3.6.5 0.703
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.702
1rj9 GCPSignal recognition particle receptor FtsY / 0.702
3c41 ANPAmino acid ABC transporter / 0.702
4c2u ANPDNA helicase / 0.702
4js0 GNPCell division control protein 42 homolog / 0.702
1b7t ADPMyosin heavy chain, striated muscle / 0.701
1ky2 GNPGTP-binding protein YPT7 / 0.701
2l0x GDPGTP-binding protein Rheb / 0.701
3oee ANPATP synthase subunit alpha, mitochondrial / 0.701
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.701
3t1t GDPProbable gliding protein mglA / 0.701
4dsn GCPGTPase KRas / 0.701
4luc GDPGTPase KRas / 0.701
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.700
4dlw GNPGTPase HRas / 0.700
2ad5 ADPCTP synthase / 0.699
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.699
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.699
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.699
3x1w GDPRas-related protein Rap-1b / 0.699
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.699
5d3q GDPDynamin-1 3.6.5.5 0.699
1wdt GTPElongation factor G (EF-G-2) / 0.698
2rgc GNPGTPase HRas / 0.698
3tlx ADPAdenylate kinase 2 / 0.698
4d0l GSPRas-related protein Rab-11A / 0.698
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.698
3kkq GDPRas-related protein M-Ras / 0.697
3l1c ADPProtein claret segregational / 0.697
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.697
4dxa GSPRas-related protein Rap-1b / 0.697
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.696
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.696
2fg5 GNPRas-related protein Rab-31 / 0.696
4l9s GDPGTPase HRas / 0.696
1z0f GDPRas-related protein Rab-14 / 0.695
4dlz GNPGTPase HRas / 0.695
4epw GDPGTPase KRas / 0.695
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.695
3ref GDPRho family GTPase / 0.694
4lpk GDPGTPase KRas / 0.694
4xvr GNPGTPase HRas / 0.694
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.693
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.693
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.693
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.693
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.693
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.692
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.692
4ys0 ADPProtein translocase subunit SecA / 0.692
2dft ADPShikimate kinase 2.7.1.71 0.691
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.691
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.691
2qen ADPWalker-Type ATPase / 0.690
3r9x GNPGTPase Era / 0.690
4hse ADPChaperone protein ClpB / 0.690
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.689
2zrj AGSProtein RecA / 0.689
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.688
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
1zc3 GNPRas-related protein Ral-A / 0.688
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.688
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.688
3q9l ATPSeptum site-determining protein MinD / 0.688
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.687
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.687
3eg5 GNPCell division control protein 42 homolog / 0.686
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.686
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.685
3rs7 GNPGTPase HRas / 0.685
5fl3 ADPPili retraction protein PilT / 0.685
2q2z ADPKinesin-like protein KIF11 / 0.684
4a28 ADPKinesin-like protein KIF11 / 0.684
1ii6 ADPKinesin-like protein KIF11 / 0.683
1svw GTPProbable GTP-binding protein EngB / 0.683
1z0d GDPRas-related protein Rab-5C / 0.683
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.683
4qbh AP5Adenylate kinase / 0.683
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.683
2cea ADPATP-dependent zinc metalloprotease FtsH / 0.682
2xto GDPGTPase IMAP family member 2 / 0.682
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.682
4uxj TTPThymidine kinase / 0.682
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.681
1svl ADPLarge T antigen 3.6.4 0.681
1yzq GNPRas-related protein Rab-6A / 0.681
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.681
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.681
3hqd ANPKinesin-like protein KIF11 / 0.681
3lbh GNPGTPase HRas / 0.681
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.681
1z0a GDPRas-related protein Rab-2A / 0.680
2zsa ADPPantothenate kinase 2.7.1.33 0.680
4dlx GNPGTPase HRas / 0.680
1uad GNPRas-related protein Ral-A / 0.679
1yrs ADPKinesin-like protein KIF11 / 0.679
3k3b ADPKinesin-like protein KIF11 / 0.679
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.678
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.678
3kuc GDPRas-related protein Rap-1A / 0.677
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.676
2a5y ATPCell death protein 4 / 0.676
2j7p GNPSignal recognition particle protein / 0.676
2j7p GNPSignal recognition particle receptor FtsY / 0.676
3dzd ADPTranscriptional regulator (NtrC family) / 0.676
1w5t ADPORC1-type DNA replication protein 2 / 0.673
2osb AP5Adenylate kinase / 0.673
1ank ANPAdenylate kinase / 0.672
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.672
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.672
2eck ADPAdenylate kinase / 0.671
4xvq GNPGTPase HRas / 0.671
1x1r GDPRas-related protein M-Ras / 0.670
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.669
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.669
4dlv GNPGTPase HRas / 0.669
1esn ANPPantothenate kinase 2.7.1.33 0.668
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.668
1l8q ADPChromosomal replication initiator protein DnaA / 0.668
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.668
2vp0 TTPDeoxynucleoside kinase / 0.668
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.668
4jld ADPAdenylate kinase / 0.668
2oo7 AP5Adenylate kinase / 0.667
4o3m ADPBloom syndrome protein 3.6.4.12 0.667
1e4y AP5Adenylate kinase / 0.666
4dso GSPGTPase KRas / 0.666
1okk GCPSignal recognition particle protein / 0.664
1okk GCPSignal recognition particle receptor FtsY / 0.664
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.664
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.663
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.663
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.663
1a4r GNHCell division control protein 42 homolog / 0.662
4y0v GDPADP-ribosylation factor 1, putative / 0.662
4ylg GDPADP-ribosylation factor 1, putative / 0.662
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.661
2iut AGSDNA translocase FtsK / 0.661
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.660
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.660
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
4ike ADPAdenylate kinase / 0.659
4ol0 GTPGTP-binding nuclear protein Ran / 0.658
2zts ADPUncharacterized protein / 0.657
4ap0 ADPKinesin-like protein KIF11 / 0.657
4mkh AP5Adenylate kinase / 0.657
5da9 AGSUncharacterized protein / 0.657
2zet GTPRas-related protein Rab-27B / 0.656
1sxj AGSReplication factor C subunit 1 / 0.655
2c9o ADPRuvB-like 1 3.6.4.12 0.655
2d7d ADPUvrABC system protein B / 0.655
3ea5 GDPGTP-binding nuclear protein Ran / 0.654
4fvq ATPTyrosine-protein kinase JAK2 / 0.654
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.653
1k5d GNPGTP-binding nuclear protein Ran / 0.653
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.653
3r9i ADPSeptum site-determining protein MinD / 0.653
1ny5 ADPTranscriptional regulator (NtrC family) / 0.651
4qbg AP5Adenylate kinase / 0.650