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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
3fvq ATP Fe(3+) ions import ATP-binding protein FbpC

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 1.213
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.986
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.978
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.891
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.889
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.883
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.881
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.873
1t91 GTPRas-related protein Rab-7a / 0.855
3w3z GTPGTP-binding nuclear protein Ran / 0.841
2r6g ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.839
1wa5 GTPGTP-binding nuclear protein Ran / 0.829
3wyf GTPGTP-binding nuclear protein / 0.829
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.825
3tkl GTPRas-related protein Rab-1A / 0.823
4qxa GTPRas-related protein Rab-9A / 0.817
1wdt GTPElongation factor G (EF-G-2) / 0.809
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.807
2bku GTPGTP-binding nuclear protein Ran / 0.803
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.800
2c5l GTPGTPase HRas / 0.799
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.798
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.793
5dac AGSUncharacterized protein / 0.791
4xoi GTPTransforming protein RhoA / 0.790
4ol0 GTPGTP-binding nuclear protein Ran / 0.789
1fmw ATPMyosin-2 heavy chain / 0.787
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.787
1a2b GSPTransforming protein RhoA / 0.785
4nyj GNPGTPase HRas / 0.784
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.783
3bc1 GNPRas-related protein Rab-27A / 0.783
1s1c GNPTransforming protein RhoA / 0.777
1cxz GSPTransforming protein RhoA / 0.776
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.776
1mmg AGSMyosin-2 heavy chain / 0.774
4mit GTPRho-related protein racC / 0.774
4xsg GSPTransforming protein RhoA / 0.773
2gcp GSPRho-related GTP-binding protein RhoC / 0.772
1gwn GTPRho-related GTP-binding protein RhoE / 0.771
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.771
1kmq GNPTransforming protein RhoA / 0.766
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.766
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.765
4js0 GNPCell division control protein 42 homolog / 0.765
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.764
4dzz ADPPlasmid partitioning protein ParF / 0.764
1v8k ANPKinesin-like protein KIF2C / 0.763
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.762
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.761
2fg5 GNPRas-related protein Rab-31 / 0.756
4dso GSPGTPase KRas / 0.754
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.753
3mjh GTPRas-related protein Rab-5A / 0.753
4nh0 ATPESX secretion system protein EccC / 0.753
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.753
1g17 GNPRas-related protein SEC4 / 0.752
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.751
4v02 ATPSite-determining protein / 0.751
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.750
4qm6 GTPMetallophosphoesterase / 0.750
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.750
2cls GTPRho-related GTP-binding protein Rho6 / 0.748
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.748
4k81 GTPGTPase HRas / 0.747
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.747
5dha GNPGTP-binding nuclear protein Ran / 0.746
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.744
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.744
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.743
2gil GTPRas-related protein Rab-6A / 0.743
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.742
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.742
1xmv ADPProtein RecA / 0.741
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.741
4d0l GSPRas-related protein Rab-11A / 0.741
1zbd GTPRas-related protein Rab-3A / 0.738
4gp6 ADPMetallophosphoesterase / 0.738
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.738
1b7t ADPMyosin heavy chain, striated muscle / 0.737
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.737
2uyi ADPKinesin-like protein KIF11 / 0.737
3hqd ANPKinesin-like protein KIF11 / 0.737
4pjk ADPMyosin-2 heavy chain / 0.737
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.736
1z0f GDPRas-related protein Rab-14 / 0.736
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.736
3kz1 GSPTransforming protein RhoA / 0.735
3e5h GNPRas-related protein Rab-28 / 0.734
4ldj GDPGTPase KRas / 0.734
2cl6 CAGGTPase HRas / 0.732
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.730
4kvg GTPRas-related protein Rap-1A / 0.730
5ftc ADPTPR domain protein / 0.730
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.729
1k5d GNPGTP-binding nuclear protein Ran / 0.728
2y65 ADPKinesin heavy chain / 0.728
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.728
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.726
1sdm ADPKinesin heavy chain-like protein / 0.726
1svl ADPLarge T antigen 3.6.4 0.726
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.724
2xae ADPKinesin-like protein KIF11 / 0.724
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.724
4luc GDPGTPase KRas / 0.724
4obe GDPGTPase KRas / 0.724
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.723
2zfi ADPKinesin-like protein KIF1A / 0.723
4ihq ADPConserved Archaeal protein / 0.723
4pk4 ADPUnconventional myosin-VI / 0.723
1z2c GNPRho-related GTP-binding protein RhoC / 0.722
2x7e ADPKinesin-like protein KIF11 / 0.722
4ql3 GDPGTPase KRas / 0.722
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.721
1jx2 ADPMyosin-2 heavy chain / 0.720
3r9x GNPGTPase Era / 0.719
4o25 GTPGTP-binding protein Rheb / 0.719
2ce2 GDPGTPase HRas / 0.718
4nyi GNPGTPase HRas / 0.718
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.716
4hut ATPCob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 0.716
1m7b GTPRho-related GTP-binding protein RhoE / 0.712
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.712
2j7p GNPSignal recognition particle protein / 0.711
2j7p GNPSignal recognition particle receptor FtsY / 0.711
1svm ATPLarge T antigen 3.6.4 0.710
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.707
4jsy GTPMetallophosphoesterase / 0.707
4xvu ATPATPase GET3 / 0.707
3l9h ADPKinesin-like protein KIF11 / 0.706
4pjj ADPUnconventional myosin-VI / 0.705
4dvg GSPRho family GTPase / 0.704
4pfp ADPUnconventional myosin-VI / 0.704
2xtn GTPGTPase IMAP family member 2 / 0.703
2r9v ATPATP synthase subunit alpha / 0.702
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.701
1yzq GNPRas-related protein Rab-6A / 0.701
1p3j AP5Adenylate kinase / 0.700
1sxj AGSReplication factor C subunit 1 / 0.700
2ffq GSPRas-related protein Rab-6B / 0.700
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.700
4asu ADPATP synthase subunit alpha, mitochondrial / 0.700
2fna ADPUncharacterized protein / 0.699
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.699
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.699
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.698
1xts GTPGTP-binding protein Rheb / 0.697
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.696
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.696
1d5c GDPGTPase (Rab6) / 0.695
1yrs ADPKinesin-like protein KIF11 / 0.694
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.694
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.694
4d81 ADPAAA ATPase, central domain protein / 0.694
4fvr ATPTyrosine-protein kinase JAK2 / 0.694
1mma ADPMyosin-2 heavy chain / 0.693
1svw GTPProbable GTP-binding protein EngB / 0.693
3m0e ATPTranscriptional regulator (NtrC family) / 0.693
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.693
1rj9 GCPSignal recognition particle receptor FtsY / 0.692
3a6p GTPGTP-binding nuclear protein Ran / 0.692
4i1v ADPDephospho-CoA kinase / 0.692
4mkf AP5Adenylate kinase / 0.692
1w5t ANPORC1-type DNA replication protein 2 / 0.691
2c96 ATPPsp operon transcriptional activator / 0.691
2pg2 ADPKinesin-like protein KIF11 / 0.691
2x2r ADPKinesin-like protein KIF11 / 0.691
3t1t GDPProbable gliding protein mglA / 0.691
4lpk GDPGTPase KRas / 0.691
2qaj AP5Adenylate kinase / 0.689
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.688
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
1x1r GDPRas-related protein M-Ras / 0.688
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.688
1e0j ANPDNA primase/helicase 2.7.7 0.687
4b7b ADPKinesin-like protein KIF11 / 0.687
1tu3 GNPRas-related protein Rab-5A / 0.686
1yra GDPGPN-loop GTPase PAB0955 / 0.686
2eu8 AP5Adenylate kinase / 0.686
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.686
5jqg GTPTubulin alpha-1B chain / 0.686
1nly AGSCag alpha / 0.684
2dpx GDPGTP-binding protein RAD / 0.684
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.684
2zet GTPRas-related protein Rab-27B / 0.684
3bbp GTPRas-related protein Rab-6A / 0.684
4hdo GNPRas-related protein Rap-1b / 0.684
4l9s GDPGTPase HRas / 0.684
4dls GNPGTPase HRas / 0.683
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.682
4cf7 ADPAdenylate kinase / 0.682
5c46 GSPRas-related protein Rab-11A / 0.682
3q9l ATPSeptum site-determining protein MinD / 0.681
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.681
4o3m ADPBloom syndrome protein 3.6.4.12 0.681
3c41 ANPAmino acid ABC transporter / 0.680
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.680
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.680
5l3s GNPSignal recognition particle receptor FtsY / 0.680
2g1q ADPKinesin-like protein KIF11 / 0.678
1z0a GDPRas-related protein Rab-2A / 0.677
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.677
2fe4 GDPRas-related protein Rab-6B / 0.676
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.676
4q03 GDPGTPase KRas / 0.676
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.675
1okk GCPSignal recognition particle protein / 0.674
1okk GCPSignal recognition particle receptor FtsY / 0.674
2zxu DSTtRNA dimethylallyltransferase 2.5.1.75 0.674
3a58 GNPGTP-binding protein RHO1 / 0.674
3rs0 GNPGTPase HRas / 0.674
2oo7 AP5Adenylate kinase / 0.672
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.671
1mab ATPATP synthase subunit alpha, mitochondrial / 0.671
2rgx AP5Adenylate kinase / 0.671
3oiu GNPGTPase HRas / 0.671
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.671
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.670
2qen ADPWalker-Type ATPase / 0.670
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.670
1esn ANPPantothenate kinase 2.7.1.33 0.669
1ozh HE3Acetolactate synthase, catabolic 2.2.1.6 0.669
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.669
3nbz GTPGTP-binding nuclear protein Ran / 0.669
4a28 ADPKinesin-like protein KIF11 / 0.669
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.669
4ike ADPAdenylate kinase / 0.669
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.669
4tyq AP5Adenylate kinase / 0.669
1n2g APCPantothenate synthetase 6.3.2.1 0.668
2hld ANPATP synthase subunit alpha, mitochondrial / 0.668
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
2whx ADPGenome polyprotein 3.4.21.91 0.668
4hse ADPChaperone protein ClpB / 0.668
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.667
1wbb ADPDNA mismatch repair protein MutS / 0.667
4fvq ATPTyrosine-protein kinase JAK2 / 0.667
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.667
1oix GDPRas-related protein Rab-11A / 0.666
4l8g GDPGTPase KRas / 0.666
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.666
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.666
1ake AP5Adenylate kinase / 0.665
3kkq GDPRas-related protein M-Ras / 0.665
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.665
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.665
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.664
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.664
4zol GTPTubulin alpha-1B chain / 0.664
2osb AP5Adenylate kinase / 0.663
2pyw ADPMethylthioribose kinase 2.7.1.100 0.663
2rgg GNPGTPase HRas / 0.663
4y0v GDPADP-ribosylation factor 1, putative / 0.663
4ylg GDPADP-ribosylation factor 1, putative / 0.663
5da9 AGSUncharacterized protein / 0.663
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.662
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.662
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.661
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
1xtr GNPGTP-binding protein Rheb / 0.661
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.661
3r9i ADPSeptum site-determining protein MinD / 0.661
3hiy UTPUncharacterized protein / 0.659
4dlv GNPGTPase HRas / 0.659
4iij GTPTubulin alpha-1B chain / 0.659
5i4n ATPTyrosine-protein kinase JAK2 / 0.659
2xto GDPGTPase IMAP family member 2 / 0.658
3cph GDPRas-related protein SEC4 / 0.658
1pzg A3DLactate dehydrogenase / 0.657
1sow NADL-lactate dehydrogenase 1.1.1.27 0.657
2rgc GNPGTPase HRas / 0.657
3q2k NAIProbable oxidoreductase / 0.657
1y9d TPPPyruvate oxidase 1.2.3.3 0.656
3k3b ADPKinesin-like protein KIF11 / 0.656
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.655
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
1g16 GDPRas-related protein SEC4 / 0.655
3pcr GTPADP-ribosylation factor 6 / 0.655
4dlt GNPGTPase HRas / 0.655
1pzh NADLactate dehydrogenase / 0.654
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.654
2ez9 TDKPyruvate oxidase 1.2.3.3 0.654
2l0x GDPGTP-binding protein Rheb / 0.654
2npi ATPmRNA cleavage and polyadenylation factor CLP1 / 0.654
4w5j AP5Adenylate kinase / 0.654
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.653
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
4ceg ADPAurora kinase A 2.7.11.1 0.653
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.653
5la6 GTPTubulin alpha-1B chain / 0.653
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.652
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.652
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.652
2pui ADPMethylthioribose kinase 2.7.1.100 0.651
4ap0 ADPKinesin-like protein KIF11 / 0.651
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.650
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.650
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.650
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.650
4n3b 12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / 0.650