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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
4qnr ATP Psp operon transcriptional activator

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4qnr ATPPsp operon transcriptional activator / 1.068
2c96 ATPPsp operon transcriptional activator / 0.888
4qos ADPPsp operon transcriptional activator / 0.869
3m0e ATPTranscriptional regulator (NtrC family) / 0.836
1p3j AP5Adenylate kinase / 0.795
2c9c ATPPsp operon transcriptional activator / 0.786
1a2b GSPTransforming protein RhoA / 0.781
2ffq GSPRas-related protein Rab-6B / 0.778
4qbg AP5Adenylate kinase / 0.773
3ftq GNPSeptin-2 / 0.772
1zio AP5Adenylate kinase / 0.771
4qm6 GTPMetallophosphoesterase / 0.770
2rgx AP5Adenylate kinase / 0.769
1ake AP5Adenylate kinase / 0.766
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.761
1tu3 GNPRas-related protein Rab-5A / 0.755
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.755
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.752
1zbd GTPRas-related protein Rab-3A / 0.751
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.751
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.750
4dvg GSPRho family GTPase / 0.750
2osb AP5Adenylate kinase / 0.748
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.746
4tyq AP5Adenylate kinase / 0.746
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.744
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.743
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.742
5dha GNPGTP-binding nuclear protein Ran / 0.738
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.737
4k81 GTPGTPase HRas / 0.737
4xsg GSPTransforming protein RhoA / 0.737
2cls GTPRho-related GTP-binding protein Rho6 / 0.736
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.735
2bc9 GNPGuanylate-binding protein 1 / 0.734
2eu8 AP5Adenylate kinase / 0.733
4jsy GTPMetallophosphoesterase / 0.732
2r9v ATPATP synthase subunit alpha / 0.731
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.730
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.730
2cl6 CAGGTPase HRas / 0.729
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.727
1w5t ANPORC1-type DNA replication protein 2 / 0.727
1fnn ADPORC1-type DNA replication protein / 0.725
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.723
1cxz GSPTransforming protein RhoA / 0.722
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.722
2qaj AP5Adenylate kinase / 0.719
3c41 ANPAmino acid ABC transporter / 0.719
4d0l GSPRas-related protein Rab-11A / 0.719
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.718
1s1c GNPTransforming protein RhoA / 0.716
1zc4 GNPRas-related protein Ral-A / 0.716
2q2z ADPKinesin-like protein KIF11 / 0.716
2gcp GSPRho-related GTP-binding protein RhoC / 0.715
4idn GNPAtlastin-1 3.6.5 0.715
1t91 GTPRas-related protein Rab-7a / 0.714
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.713
2oo7 AP5Adenylate kinase / 0.712
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.711
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.711
3dl0 AP5Adenylate kinase / 0.711
1mab ATPATP synthase subunit alpha, mitochondrial / 0.710
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.710
2gm1 ADPKinesin-like protein KIF11 / 0.709
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.709
3kz1 GSPTransforming protein RhoA / 0.708
3tkl GTPRas-related protein Rab-1A / 0.707
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.707
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.706
4kvg GTPRas-related protein Rap-1A / 0.706
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.705
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.705
4qxa GTPRas-related protein Rab-9A / 0.705
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.705
5c46 GSPRas-related protein Rab-11A / 0.705
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.704
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.704
2gil GTPRas-related protein Rab-6A / 0.703
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.703
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.703
1m7b GTPRho-related GTP-binding protein RhoE / 0.702
4cf7 ADPAdenylate kinase / 0.702
4mit GTPRho-related protein racC / 0.702
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.702
2bku GTPGTP-binding nuclear protein Ran / 0.701
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.701
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.701
4x8l AP5Adenylate kinase / 0.700
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.699
1wa5 GTPGTP-binding nuclear protein Ran / 0.699
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.699
3bc1 GNPRas-related protein Rab-27A / 0.699
3myk ANPMyosin-2 heavy chain / 0.699
3r9x GNPGTPase Era / 0.699
5ftc ADPTPR domain protein / 0.697
2fg5 GNPRas-related protein Rab-31 / 0.696
3qbt GNPRas-related protein Rab-8A / 0.696
4ww4 ADPRuvB-like helicase / 0.696
4xoi GTPTransforming protein RhoA / 0.696
1gwn GTPRho-related GTP-binding protein RhoE / 0.695
1wdt GTPElongation factor G (EF-G-2) / 0.695
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.695
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
2fl2 ADPKinesin-like protein KIF11 / 0.695
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.695
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.694
2jlr ANPGenome polyprotein 3.4.21.91 0.693
2c5l GTPGTPase HRas / 0.692
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.692
2zet GTPRas-related protein Rab-27B / 0.692
4nh0 ATPESX secretion system protein EccC / 0.692
5da9 AGSUncharacterized protein / 0.692
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.691
2xul ATPNitrogen regulatory protein P-II / 0.691
2hld ANPATP synthase subunit alpha, mitochondrial / 0.690
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
3b1x GNPFerrous iron transport protein B / 0.690
2bbw GP5Adenylate kinase 4, mitochondrial / 0.689
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.689
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
3w3z GTPGTP-binding nuclear protein Ran / 0.689
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
2x7e ADPKinesin-like protein KIF11 / 0.688
3g6x DGTDNA polymerase iota 2.7.7.7 0.688
3hqd ANPKinesin-like protein KIF11 / 0.688
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.687
3k3b ADPKinesin-like protein KIF11 / 0.687
3thy ADPDNA mismatch repair protein Msh2 / 0.687
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.687
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.686
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.686
3akd CDPCytidylate kinase / 0.686
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.686
4o2l GTPGTP-binding protein Rheb / 0.686
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.686
4pk4 ADPUnconventional myosin-VI / 0.686
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.685
1g17 GNPRas-related protein SEC4 / 0.685
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.685
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.685
3nbx ADPATPase RavA 3.6.3 0.685
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.684
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.684
3wyf GTPGTP-binding nuclear protein / 0.684
4b7b ADPKinesin-like protein KIF11 / 0.684
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.683
4db1 ANPMyosin-7 / 0.683
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.683
1sxj AGSReplication factor C subunit 1 / 0.682
3eg5 GNPCell division control protein 42 homolog / 0.682
1fmw ATPMyosin-2 heavy chain / 0.681
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.681
1xmv ADPProtein RecA / 0.681
2jcs TTPDeoxynucleoside kinase / 0.681
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.680
4dsu GDPGTPase KRas / 0.680
3k1j ADPATP-dependent protease Lon / 0.679
4ol0 GTPGTP-binding nuclear protein Ran / 0.679
3bbp GTPRas-related protein Rab-6A / 0.678
5l3s GNPSignal recognition particle receptor FtsY / 0.678
1z2c GNPRho-related GTP-binding protein RhoC / 0.677
3bxz ADPProtein translocase subunit SecA / 0.677
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.677
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.677
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.676
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.676
4dso GSPGTPase KRas / 0.676
3mjh GTPRas-related protein Rab-5A / 0.675
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.674
4g0n GNPGTPase HRas / 0.674
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.674
2uyi ADPKinesin-like protein KIF11 / 0.673
2xae ADPKinesin-like protein KIF11 / 0.673
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.672
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.672
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.671
1lfd GNPGTPase HRas / 0.670
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.670
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.670
3l1c ADPProtein claret segregational / 0.670
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.670
4l16 ADPFidgetin-like protein 1 3.6.4 0.670
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.669
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.669
2uz3 TTPThymidine kinase / 0.669
2y65 ADPKinesin heavy chain / 0.669
3d8b ADPFidgetin-like protein 1 3.6.4 0.669
4c2u ANPDNA helicase / 0.669
4o25 GTPGTP-binding protein Rheb / 0.669
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.668
4uj5 GNPRas-related protein Rab-11A / 0.668
1nly AGSCag alpha / 0.667
2xsz ATPRuvB-like 2 3.6.4.12 0.667
3q5d GDPAtlastin-1 3.6.5 0.667
3uk6 ADPRuvB-like 2 3.6.4.12 0.667
2g1q ADPKinesin-like protein KIF11 / 0.666
2ql6 ADPNicotinamide riboside kinase 1 / 0.666
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.665
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.665
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.665
3bxo UPPdTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose / 0.664
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.663
2dpx GDPGTP-binding protein RAD / 0.663
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.663
2x2r ADPKinesin-like protein KIF11 / 0.663
2zro ADPProtein RecA / 0.663
3dkv AP5Adenylate kinase / 0.663
4hse ADPChaperone protein ClpB / 0.663
3jvv ACPTwitching mobility protein / 0.662
4l9s GDPGTPase HRas / 0.662
4lv6 GDPGTPase KRas / 0.662
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.661
1yrs ADPKinesin-like protein KIF11 / 0.661
2j9g ADPBiotin carboxylase 6.3.4.14 0.661
2q16 ITTdITP/XTP pyrophosphatase / 0.661
4khy TTPDNA-directed DNA polymerase / 0.661
2ce2 GDPGTPase HRas / 0.660
4dlv GNPGTPase HRas / 0.660
4dxa GSPRas-related protein Rap-1b / 0.660
1oix GDPRas-related protein Rab-11A / 0.659
1z0d GDPRas-related protein Rab-5C / 0.659
2l0x GDPGTP-binding protein Rheb / 0.659
2zrf DTPProtein RecA / 0.659
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.659
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.659
1esn ANPPantothenate kinase 2.7.1.33 0.658
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.658
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.658
4a28 ADPKinesin-like protein KIF11 / 0.658
1g16 GDPRas-related protein SEC4 / 0.657
2nmv ADPUvrABC system protein B / 0.657
2zrj AGSProtein RecA / 0.657
4fjl DGTDNA-directed DNA polymerase / 0.657
4iij GTPTubulin alpha-1B chain / 0.657
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.657
5ftf ADPTPR domain protein / 0.657
1sdm ADPKinesin heavy chain-like protein / 0.656
4fjj TTPDNA-directed DNA polymerase / 0.656
4fjm DCPDNA-directed DNA polymerase / 0.656
4o3m ADPBloom syndrome protein 3.6.4.12 0.656
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.655
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
3mhy ATPNitrogen regulatory protein P-II 1 / 0.654
3q9l ATPSeptum site-determining protein MinD / 0.654
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.653
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.652
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
1kqm ANPMyosin heavy chain, striated muscle / 0.652
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.652
5aun ADPIron-sulfur cluster carrier protein / 0.652
5dac AGSUncharacterized protein / 0.652
1okk GCPSignal recognition particle protein / 0.651
1okk GCPSignal recognition particle receptor FtsY / 0.651
2aky AP5Adenylate kinase / 0.651
2eck ADPAdenylate kinase / 0.650
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.650
4fh5 UTPTerminal uridylyltransferase cid1 / 0.650