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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
2c9c ATP Psp operon transcriptional activator

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2c9c ATPPsp operon transcriptional activator / 1.014
2c96 ATPPsp operon transcriptional activator / 0.905
4qos ADPPsp operon transcriptional activator / 0.873
4ww4 ADPRuvB-like helicase / 0.795
1w5s ADPORC1-type DNA replication protein 2 / 0.794
4qnr ATPPsp operon transcriptional activator / 0.786
1ake AP5Adenylate kinase / 0.773
1ny5 ADPTranscriptional regulator (NtrC family) / 0.767
1w5t ANPORC1-type DNA replication protein 2 / 0.766
5aun ADPIron-sulfur cluster carrier protein / 0.759
5ftc ADPTPR domain protein / 0.754
1gwn GTPRho-related GTP-binding protein RhoE / 0.749
4c2u ANPDNA helicase / 0.743
1m7b GTPRho-related GTP-binding protein RhoE / 0.742
2gm1 ADPKinesin-like protein KIF11 / 0.742
2r9v ATPATP synthase subunit alpha / 0.742
2x2r ADPKinesin-like protein KIF11 / 0.741
1mab ATPATP synthase subunit alpha, mitochondrial / 0.740
1fnn ADPORC1-type DNA replication protein / 0.737
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.735
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.735
4jsy GTPMetallophosphoesterase / 0.735
4xoi GTPTransforming protein RhoA / 0.735
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.734
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.733
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.733
2gil GTPRas-related protein Rab-6A / 0.733
2uyi ADPKinesin-like protein KIF11 / 0.732
4asu ADPATP synthase subunit alpha, mitochondrial / 0.732
2ffq GSPRas-related protein Rab-6B / 0.731
4dso GSPGTPase KRas / 0.731
2x7e ADPKinesin-like protein KIF11 / 0.730
2bc9 GNPGuanylate-binding protein 1 / 0.728
2c5l GTPGTPase HRas / 0.728
2bku GTPGTP-binding nuclear protein Ran / 0.727
4idn GNPAtlastin-1 3.6.5 0.726
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.724
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.724
4dxa GSPRas-related protein Rap-1b / 0.722
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.722
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.722
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.721
4dsu GDPGTPase KRas / 0.721
4idp GNPAtlastin-1 3.6.5 0.721
2hld ANPATP synthase subunit alpha, mitochondrial / 0.720
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.720
2zr9 DTPProtein RecA / 0.720
2xsz ATPRuvB-like 2 3.6.4.12 0.718
4o25 GTPGTP-binding protein Rheb / 0.718
4qbg AP5Adenylate kinase / 0.718
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.717
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.716
3uk6 ADPRuvB-like 2 3.6.4.12 0.716
4mit GTPRho-related protein racC / 0.716
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.715
2gcp GSPRho-related GTP-binding protein RhoC / 0.715
3b1x GNPFerrous iron transport protein B / 0.714
4kvg GTPRas-related protein Rap-1A / 0.714
5c46 GSPRas-related protein Rab-11A / 0.714
3w3z GTPGTP-binding nuclear protein Ran / 0.713
1t91 GTPRas-related protein Rab-7a / 0.712
3mjh GTPRas-related protein Rab-5A / 0.712
1tu3 GNPRas-related protein Rab-5A / 0.711
4d0l GSPRas-related protein Rab-11A / 0.711
5dif GNPGTP-binding nuclear protein Ran / 0.711
1mmg AGSMyosin-2 heavy chain / 0.709
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.709
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.709
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.709
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
4dlt GNPGTPase HRas / 0.708
4ql3 GDPGTPase KRas / 0.708
1xts GTPGTP-binding protein Rheb / 0.707
3lbn GNPGTPase HRas / 0.707
4dlw GNPGTPase HRas / 0.707
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.706
2rgc GNPGTPase HRas / 0.706
3oiv GNPGTPase HRas / 0.706
3rs5 GNPGTPase HRas / 0.706
4dls GNPGTPase HRas / 0.706
4dlx GNPGTPase HRas / 0.706
4l9w GNPGTPase HRas / 0.706
4xsg GSPTransforming protein RhoA / 0.706
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.705
4jld ADPAdenylate kinase / 0.705
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.704
2fe4 GDPRas-related protein Rab-6B / 0.704
3x1w GDPRas-related protein Rap-1b / 0.704
4q03 GDPGTPase KRas / 0.704
1ii6 ADPKinesin-like protein KIF11 / 0.703
4jl5 ADPAdenylate kinase / 0.703
4lpk GDPGTPase KRas / 0.703
4tq9 GDPGTPase KRas / 0.703
1cxz GSPTransforming protein RhoA / 0.702
3pit GNPRas-related protein M-Ras / 0.702
4d81 ADPAAA ATPase, central domain protein / 0.702
1a2b GSPTransforming protein RhoA / 0.701
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.701
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.701
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.700
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.700
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.700
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.699
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.699
4g0n GNPGTPase HRas / 0.698
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.697
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.697
3law GNPRas-related protein Rab-7a / 0.697
4cym GCPRas-related protein Rab-32 / 0.697
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.697
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.696
2y65 ADPKinesin heavy chain / 0.696
3a58 GNPGTP-binding protein RHO1 / 0.695
3a6p GTPGTP-binding nuclear protein Ran / 0.695
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.695
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.695
1vg8 GNPRas-related protein Rab-7a / 0.694
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.694
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.694
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.694
1ibr GNPGTP-binding nuclear protein Ran / 0.693
2ce2 GDPGTPase HRas / 0.693
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.693
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.693
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.693
3lbi GNPGTPase HRas / 0.692
4epx GDPGTPase KRas / 0.692
4gp6 ADPMetallophosphoesterase / 0.692
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.691
3rs0 GNPGTPase HRas / 0.691
3rs4 GNPGTPase HRas / 0.691
3rsl GNPGTPase HRas / 0.691
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.691
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.691
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.690
2zrj AGSProtein RecA / 0.690
3ftq GNPSeptin-2 / 0.690
3oiw GNPGTPase HRas / 0.690
3rs7 GNPGTPase HRas / 0.690
4a1z ADPKinesin-like protein KIF11 / 0.690
4dlz GNPGTPase HRas / 0.690
4nyj GNPGTPase HRas / 0.690
4dvg GSPRho family GTPase / 0.689
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.689
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.688
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.688
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
4jlo ADPAdenylate kinase / 0.688
1ow3 GDPTransforming protein RhoA / 0.687
1fmw ATPMyosin-2 heavy chain / 0.686
1lfd GNPGTPase HRas / 0.686
3tkl GTPRas-related protein Rab-1A / 0.686
3k1j ADPATP-dependent protease Lon / 0.684
3nbx ADPATPase RavA 3.6.3 0.684
3qbt GNPRas-related protein Rab-8A / 0.684
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.683
4js0 GNPCell division control protein 42 homolog / 0.683
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.683
1w5t ADPORC1-type DNA replication protein 2 / 0.682
4dsn GCPGTPase KRas / 0.682
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.681
3myk ANPMyosin-2 heavy chain / 0.681
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.681
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.681
2q3f GNPRas-related GTP-binding protein D / 0.680
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.680
4k81 GTPGTPase HRas / 0.680
1kmq GNPTransforming protein RhoA / 0.679
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.679
2jcs TTPDeoxynucleoside kinase / 0.679
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.679
3dzd ADPTranscriptional regulator (NtrC family) / 0.679
3kkq GDPRas-related protein M-Ras / 0.679
4v02 ATPSite-determining protein / 0.679
3kko GNPRas-related protein M-Ras / 0.678
5da9 AGSUncharacterized protein / 0.678
1zbd GTPRas-related protein Rab-3A / 0.677
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.677
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.676
1z0d GDPRas-related protein Rab-5C / 0.676
2bbw GP5Adenylate kinase 4, mitochondrial / 0.676
2zet GTPRas-related protein Rab-27B / 0.676
1n6l GTPRas-related protein Rab-5A / 0.675
1yzq GNPRas-related protein Rab-6A / 0.675
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.675
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.675
4a51 ADPKinesin-like protein KIF11 / 0.675
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.674
2fg5 GNPRas-related protein Rab-31 / 0.674
3l1c ADPProtein claret segregational / 0.673
3ref GDPRho family GTPase / 0.673
4dzz ADPPlasmid partitioning protein ParF / 0.673
4nh0 ATPESX secretion system protein EccC / 0.673
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.672
3kz1 GSPTransforming protein RhoA / 0.672
4l16 ADPFidgetin-like protein 1 3.6.4 0.672
1am4 GNPCell division control protein 42 homolog / 0.671
1sq5 ADPPantothenate kinase 2.7.1.33 0.671
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.671
4lhv GDPRas-related protein Rab-8A / 0.671
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.670
1k5d GNPGTP-binding nuclear protein Ran / 0.669
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.669
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.669
3q9l ATPSeptum site-determining protein MinD / 0.669
4nyi GNPGTPase HRas / 0.669
5fl3 ADPPili retraction protein PilT / 0.668
2cl6 CAGGTPase HRas / 0.667
2d4h 5GPGuanylate-binding protein 1 / 0.667
3k3b ADPKinesin-like protein KIF11 / 0.666
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.666
4mkf AP5Adenylate kinase / 0.666
5dha GNPGTP-binding nuclear protein Ran / 0.666
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.665
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.665
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.665
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.664
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.664
4lhw GNPRas-related protein Rab-8A / 0.664
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.662
1z0a GDPRas-related protein Rab-2A / 0.662
2zsa ADPPantothenate kinase 2.7.1.33 0.662
3lbh GNPGTPase HRas / 0.662
1b7t ADPMyosin heavy chain, striated muscle / 0.660
1zc4 GNPRas-related protein Ral-A / 0.660
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.660
1dj3 GDPAdenylosuccinate synthetase, chloroplastic / 0.659
4hdo GNPRas-related protein Rap-1b / 0.659
4qm6 GTPMetallophosphoesterase / 0.659
5b2z GNPGTPase HRas / 0.659
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.658
2vp2 DGTDeoxynucleoside kinase / 0.658
3r9x GNPGTPase Era / 0.658
4iei ADPGene 2 protein / 0.657
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.656
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.656
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.656
3thy ADPDNA mismatch repair protein Msh2 / 0.656
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.656
3d8b ADPFidgetin-like protein 1 3.6.4 0.655
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.655
4xvr GNPGTPase HRas / 0.654
4mkh AP5Adenylate kinase / 0.653
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.651
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
1oix GDPRas-related protein Rab-11A / 0.651
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.650
1nsf ATPVesicle-fusing ATPase 3.6.4.6 0.650