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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
1r0z ATP Cystic fibrosis transmembrane conductance regulator

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.953
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.832
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.779
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.769
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.767
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.766
2c5l GTPGTPase HRas / 0.763
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.761
1k5d GNPGTP-binding nuclear protein Ran / 0.758
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.758
1svm ATPLarge T antigen 3.6.4 0.751
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.751
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.750
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.749
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.748
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.747
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.746
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.743
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.742
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.742
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.741
1w5t ANPORC1-type DNA replication protein 2 / 0.740
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.739
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.739
3tkl GTPRas-related protein Rab-1A / 0.738
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.738
1t91 GTPRas-related protein Rab-7a / 0.737
1wa5 GTPGTP-binding nuclear protein Ran / 0.737
2xae ADPKinesin-like protein KIF11 / 0.736
2y65 ADPKinesin heavy chain / 0.736
3myk ANPMyosin-2 heavy chain / 0.736
4luc GDPGTPase KRas / 0.736
2gcp GSPRho-related GTP-binding protein RhoC / 0.735
4xsg GSPTransforming protein RhoA / 0.735
2ffq GSPRas-related protein Rab-6B / 0.734
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.732
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.732
3wyf GTPGTP-binding nuclear protein / 0.732
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.731
1m7b GTPRho-related GTP-binding protein RhoE / 0.731
2fg5 GNPRas-related protein Rab-31 / 0.731
1cxz GSPTransforming protein RhoA / 0.730
1gwn GTPRho-related GTP-binding protein RhoE / 0.730
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.728
4kvg GTPRas-related protein Rap-1A / 0.728
2zts ADPUncharacterized protein / 0.727
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.726
4cym GCPRas-related protein Rab-32 / 0.726
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.725
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.725
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.725
5dif GNPGTP-binding nuclear protein Ran / 0.725
1xmv ADPProtein RecA / 0.724
1a2b GSPTransforming protein RhoA / 0.723
1s1c GNPTransforming protein RhoA / 0.723
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.723
3rab GNPRas-related protein Rab-3A / 0.723
4qm6 GTPMetallophosphoesterase / 0.722
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.722
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.721
1sdm ADPKinesin heavy chain-like protein / 0.720
2whx ADPGenome polyprotein 3.4.21.91 0.720
1xts GTPGTP-binding protein Rheb / 0.719
3a58 GNPGTP-binding protein RHO1 / 0.719
4hut ATPCob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 0.719
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.718
3cob ADPKinesin heavy chain-like protein / 0.718
3tso GNPRas-related protein Rab-25 / 0.718
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.717
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.717
2zfi ADPKinesin-like protein KIF1A / 0.717
3bc1 GNPRas-related protein Rab-27A / 0.717
4goj GNPADP-ribosylation factor-like protein 3 / 0.717
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.716
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.716
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.716
4v02 ATPSite-determining protein / 0.716
1jx2 ADPMyosin-2 heavy chain / 0.715
1ky2 GNPGTP-binding protein YPT7 / 0.715
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.715
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.715
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.715
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.715
3e5h GNPRas-related protein Rab-28 / 0.715
5di3 GNPADP-ribosylation factor-like protein 3 / 0.715
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.714
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.714
4mkf AP5Adenylate kinase / 0.714
1fnn ADPORC1-type DNA replication protein / 0.712
2uz3 TTPThymidine kinase / 0.712
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.712
1wdt GTPElongation factor G (EF-G-2) / 0.711
2hld ANPATP synthase subunit alpha, mitochondrial / 0.711
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.711
3m0e ATPTranscriptional regulator (NtrC family) / 0.711
4nyj GNPGTPase HRas / 0.711
4qxa GTPRas-related protein Rab-9A / 0.711
4xoi GTPTransforming protein RhoA / 0.711
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.710
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.710
1vg8 GNPRas-related protein Rab-7a / 0.710
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.708
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.708
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.708
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.707
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.707
3ftq GNPSeptin-2 / 0.706
3vhx GTPADP-ribosylation factor 6 / 0.706
3zia ATPATP synthase subunit alpha, mitochondrial / 0.706
4jsy GTPMetallophosphoesterase / 0.706
1v8k ANPKinesin-like protein KIF2C / 0.705
4l8g GDPGTPase KRas / 0.705
4pjk ADPMyosin-2 heavy chain / 0.705
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.704
4ap0 ADPKinesin-like protein KIF11 / 0.704
1f5n GNPGuanylate-binding protein 1 / 0.703
1z0d GDPRas-related protein Rab-5C / 0.703
1xtr GNPGTP-binding protein Rheb / 0.702
2osb AP5Adenylate kinase / 0.702
4mkg AP5Adenylate kinase / 0.702
4obe GDPGTPase KRas / 0.702
4w5j AP5Adenylate kinase / 0.702
4y0v GDPADP-ribosylation factor 1, putative / 0.702
4ylg GDPADP-ribosylation factor 1, putative / 0.702
1ow3 GDPTransforming protein RhoA / 0.701
2bc9 GNPGuanylate-binding protein 1 / 0.701
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.701
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.701
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.701
3hqd ANPKinesin-like protein KIF11 / 0.701
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.701
4hdq GNPRas-related protein Rap-1b / 0.701
5dha GNPGTP-binding nuclear protein Ran / 0.701
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.700
5ftc ADPTPR domain protein / 0.700
1b7t ADPMyosin heavy chain, striated muscle / 0.699
2oo7 AP5Adenylate kinase / 0.699
2qaj AP5Adenylate kinase / 0.699
2uyi ADPKinesin-like protein KIF11 / 0.699
2x2r ADPKinesin-like protein KIF11 / 0.699
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.699
4qnr ATPPsp operon transcriptional activator / 0.699
1w5t ADPORC1-type DNA replication protein 2 / 0.698
1z0f GDPRas-related protein Rab-14 / 0.698
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.698
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.697
2bku GTPGTP-binding nuclear protein Ran / 0.697
2j5x GSPADP-ribosylation factor 6 / 0.697
3oee ANPATP synthase subunit alpha, mitochondrial / 0.697
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.697
4k81 GTPGTPase HRas / 0.697
4dls GNPGTPase HRas / 0.696
4ihq ADPConserved Archaeal protein / 0.696
1sq5 ADPPantothenate kinase 2.7.1.33 0.695
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.695
1zc3 GNPRas-related protein Ral-A / 0.694
3c41 ANPAmino acid ABC transporter / 0.694
1zbd GTPRas-related protein Rab-3A / 0.693
5c46 GSPRas-related protein Rab-11A / 0.693
2q3f GNPRas-related GTP-binding protein D / 0.692
4dvg GSPRho family GTPase / 0.692
4fvr ATPTyrosine-protein kinase JAK2 / 0.692
4nyi GNPGTPase HRas / 0.692
1xp8 AGSProtein RecA / 0.690
4cf7 ADPAdenylate kinase / 0.690
4lhw GNPRas-related protein Rab-8A / 0.690
4ol0 GTPGTP-binding nuclear protein Ran / 0.690
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.689
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
4dso GSPGTPase KRas / 0.688
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.687
2oap ANPType II secretion system protein (GspE-2) / 0.687
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.686
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.686
1yrs ADPKinesin-like protein KIF11 / 0.686
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.686
1e0j ANPDNA primase/helicase 2.7.7 0.685
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.685
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.685
4nh0 ATPESX secretion system protein EccC / 0.685
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.684
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
1fmw ATPMyosin-2 heavy chain / 0.684
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.684
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
1p3j AP5Adenylate kinase / 0.684
1svl ADPLarge T antigen 3.6.4 0.684
1z2c GNPRho-related GTP-binding protein RhoC / 0.684
2iut AGSDNA translocase FtsK / 0.684
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.684
4to4 DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.684
3l9h ADPKinesin-like protein KIF11 / 0.683
4jlo ADPAdenylate kinase / 0.683
4xvu ATPATPase GET3 / 0.683
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.682
1mma ADPMyosin-2 heavy chain / 0.680
3d8b ADPFidgetin-like protein 1 3.6.4 0.680
3w3z GTPGTP-binding nuclear protein Ran / 0.680
5dac AGSUncharacterized protein / 0.680
1mmg AGSMyosin-2 heavy chain / 0.679
3dkv AP5Adenylate kinase / 0.679
2aky AP5Adenylate kinase / 0.678
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.678
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.678
5aun ADPIron-sulfur cluster carrier protein / 0.678
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.677
2zro ADPProtein RecA / 0.677
4g01 GDPRas-related protein RABF2b / 0.677
1tu3 GNPRas-related protein Rab-5A / 0.676
2j7p GNPSignal recognition particle protein / 0.676
2j7p GNPSignal recognition particle receptor FtsY / 0.676
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
3tlx ADPAdenylate kinase 2 / 0.676
2gil GTPRas-related protein Rab-6A / 0.675
2xul ATPNitrogen regulatory protein P-II / 0.675
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.675
4pjj ADPUnconventional myosin-VI / 0.675
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.674
2xtn GTPGTPase IMAP family member 2 / 0.674
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.674
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.673
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.673
2gm1 ADPKinesin-like protein KIF11 / 0.672
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.672
4o25 GTPGTP-binding protein Rheb / 0.672
2rgc GNPGTPase HRas / 0.671
3mjh GTPRas-related protein Rab-5A / 0.671
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.671
4dlz GNPGTPase HRas / 0.671
4tyq AP5Adenylate kinase / 0.671
1n6l GTPRas-related protein Rab-5A / 0.670
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.670
3k1j ADPATP-dependent protease Lon / 0.670
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.669
2c9c ATPPsp operon transcriptional activator / 0.669
2jlr ANPGenome polyprotein 3.4.21.91 0.669
4gp6 ADPMetallophosphoesterase / 0.669
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.669
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.669
2r9v ATPATP synthase subunit alpha / 0.668
3qbv GDPCell division control protein 42 homolog / 0.668
4mit GTPRho-related protein racC / 0.668
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.667
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.667
4b7b ADPKinesin-like protein KIF11 / 0.667
5i4n ATPTyrosine-protein kinase JAK2 / 0.667
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.666
1zio AP5Adenylate kinase / 0.666
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.666
3ddc GNPGTPase HRas / 0.666
1n6m ADPProtein claret segregational / 0.665
3kud GDPGTPase HRas / 0.665
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.664
4dsn GCPGTPase KRas / 0.664
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.663
1yra GDPGPN-loop GTPase PAB0955 / 0.663
3mhy ATPNitrogen regulatory protein P-II 1 / 0.663
2rgx AP5Adenylate kinase / 0.662
3pit GNPRas-related protein M-Ras / 0.662
1rj9 GCPSignal recognition particle receptor FtsY / 0.661
3bxz ADPProtein translocase subunit SecA / 0.661
3dl0 AP5Adenylate kinase / 0.661
3eg5 GNPCell division control protein 42 homolog / 0.661
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.661
5cyo GDPSeptin-9 / 0.661
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.660
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.660
1w5s ADPORC1-type DNA replication protein 2 / 0.660
4pfp ADPUnconventional myosin-VI / 0.660
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.659
1okk GCPSignal recognition particle protein / 0.658
1okk GCPSignal recognition particle receptor FtsY / 0.658
1sxj AGSReplication factor C subunit 1 / 0.658
2cl6 CAGGTPase HRas / 0.658
2jas DTPDeoxyguanosine kinase / 0.658
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.658
5jlj GNPGTP-binding nuclear protein Ran / 0.658
4xvq GNPGTPase HRas / 0.657
5bn3 ADPV-type ATP synthase alpha chain / 0.657
5bn3 ADPNEQ263 / 0.657
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.657
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.656
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.656
3law GNPRas-related protein Rab-7a / 0.656
4hi0 GDPUrease accessory protein UreG / 0.656
4idn GNPAtlastin-1 3.6.5 0.656
4nu0 AP5Adenylate kinase / 0.656
2l0x GDPGTP-binding protein Rheb / 0.655
2dpx GDPGTP-binding protein RAD / 0.654
4uxj TTPThymidine kinase / 0.654
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.654
4zca ADPKinesin-like protein KIF11 / 0.654
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.654
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.653
4d0l GSPRas-related protein Rab-11A / 0.653
4dxa GSPRas-related protein Rap-1b / 0.653
4typ AP5Adenylate kinase / 0.653
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.652
3v2u ATPProtein GAL3 / 0.652
4to3 DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.652
1foa UD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase 2.4.1.101 0.650
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.650