Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
4ki0 ANP Maltose/maltodextrin import ATP-binding protein MalK

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 1.213
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.986
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.918
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.886
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.855
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.851
3bc1 GNPRas-related protein Rab-27A / 0.848
1ky2 GNPGTP-binding protein YPT7 / 0.839
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.831
1wa5 GTPGTP-binding nuclear protein Ran / 0.830
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.827
3e5h GNPRas-related protein Rab-28 / 0.825
1kmq GNPTransforming protein RhoA / 0.823
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.821
3rab GNPRas-related protein Rab-3A / 0.819
4rkf GNPRas-related protein Rab-3 / 0.817
2rgg GNPGTPase HRas / 0.815
3wyf GTPGTP-binding nuclear protein / 0.814
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.814
1k5d GNPGTP-binding nuclear protein Ran / 0.811
1n6l GTPRas-related protein Rab-5A / 0.807
5jlj GNPGTP-binding nuclear protein Ran / 0.806
1g17 GNPRas-related protein SEC4 / 0.804
3w3z GTPGTP-binding nuclear protein Ran / 0.804
3tso GNPRas-related protein Rab-25 / 0.803
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.796
4jsy GTPMetallophosphoesterase / 0.793
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.788
2bku GTPGTP-binding nuclear protein Ran / 0.788
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.788
3b1x GNPFerrous iron transport protein B / 0.788
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.788
4lhw GNPRas-related protein Rab-8A / 0.788
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.788
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.786
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.786
2bme GNPRas-related protein Rab-4A / 0.785
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.785
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.785
4dso GSPGTPase KRas / 0.784
4js0 GNPCell division control protein 42 homolog / 0.783
4qm6 GTPMetallophosphoesterase / 0.782
1v8k ANPKinesin-like protein KIF2C / 0.777
3c41 ANPAmino acid ABC transporter / 0.777
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.776
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.775
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.774
3k9l GNPGTPase HRas / 0.773
4uj3 GNPRas-related protein Rab-11A / 0.773
4cym GCPRas-related protein Rab-32 / 0.771
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.771
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.770
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.769
4goj GNPADP-ribosylation factor-like protein 3 / 0.769
3ftq GNPSeptin-2 / 0.768
3kko GNPRas-related protein M-Ras / 0.768
5dha GNPGTP-binding nuclear protein Ran / 0.768
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.767
1z2c GNPRho-related GTP-binding protein RhoC / 0.767
3lbh GNPGTPase HRas / 0.766
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.764
2q3f GNPRas-related GTP-binding protein D / 0.764
4nyi GNPGTPase HRas / 0.763
5dif GNPGTP-binding nuclear protein Ran / 0.763
1f5n GNPGuanylate-binding protein 1 / 0.762
4hdq GNPRas-related protein Rap-1b / 0.762
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.761
3qbt GNPRas-related protein Rab-8A / 0.759
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.758
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.756
1yu9 GNPRas-related protein Rab-4A / 0.756
1wdt GTPElongation factor G (EF-G-2) / 0.753
3tgp GNPGTPase HRas / 0.753
4l9w GNPGTPase HRas / 0.753
4nyj GNPGTPase HRas / 0.752
2cls GTPRho-related GTP-binding protein Rho6 / 0.751
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.751
4xoi GTPTransforming protein RhoA / 0.751
3tkl GTPRas-related protein Rab-1A / 0.750
3pit GNPRas-related protein M-Ras / 0.749
1a2b GSPTransforming protein RhoA / 0.747
4qxa GTPRas-related protein Rab-9A / 0.747
3kz1 GSPTransforming protein RhoA / 0.745
1cxz GSPTransforming protein RhoA / 0.744
1xtr GNPGTP-binding protein Rheb / 0.744
2bc9 GNPGuanylate-binding protein 1 / 0.743
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.741
1ibr GNPGTP-binding nuclear protein Ran / 0.738
2r6g ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.737
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.737
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.737
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.737
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.736
4xvq GNPGTPase HRas / 0.736
1zc3 GNPRas-related protein Ral-A / 0.734
2gil GTPRas-related protein Rab-6A / 0.734
3mjh GTPRas-related protein Rab-5A / 0.734
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.734
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.733
1zc4 GNPRas-related protein Ral-A / 0.733
4hdo GNPRas-related protein Rap-1b / 0.733
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.732
3ddc GNPGTPase HRas / 0.732
3i3s GNPGTPase HRas / 0.732
3v4f GNPGTPase HRas / 0.732
3x1z GNPRas-related protein Rap-1b / 0.732
5dac AGSUncharacterized protein / 0.732
1gwn GTPRho-related GTP-binding protein RhoE / 0.731
2c5l GTPGTPase HRas / 0.731
2rgb GNPGTPase HRas / 0.731
2rge GNPGTPase HRas / 0.731
3k8y GNPGTPase HRas / 0.731
3l8y GNPGTPase HRas / 0.731
3oiu GNPGTPase HRas / 0.731
3rs0 GNPGTPase HRas / 0.731
3rs4 GNPGTPase HRas / 0.731
3rs5 GNPGTPase HRas / 0.731
3rs7 GNPGTPase HRas / 0.731
3rsl GNPGTPase HRas / 0.731
4dls GNPGTPase HRas / 0.731
4dlt GNPGTPase HRas / 0.731
4dlv GNPGTPase HRas / 0.731
4xsg GSPTransforming protein RhoA / 0.731
2rgc GNPGTPase HRas / 0.730
4dlw GNPGTPase HRas / 0.730
4dlx GNPGTPase HRas / 0.730
4dlz GNPGTPase HRas / 0.730
5b2z GNPGTPase HRas / 0.730
3lbn GNPGTPase HRas / 0.729
3myk ANPMyosin-2 heavy chain / 0.729
3oiv GNPGTPase HRas / 0.729
3oiw GNPGTPase HRas / 0.729
3lbi GNPGTPase HRas / 0.728
4idn GNPAtlastin-1 3.6.5 0.728
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.727
3m0e ATPTranscriptional regulator (NtrC family) / 0.726
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.725
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.725
1okk GCPSignal recognition particle protein / 0.723
1okk GCPSignal recognition particle receptor FtsY / 0.723
1esn ANPPantothenate kinase 2.7.1.33 0.722
4dzz ADPPlasmid partitioning protein ParF / 0.722
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.721
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.721
1m7b GTPRho-related GTP-binding protein RhoE / 0.721
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.719
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.719
2j7p GNPSignal recognition particle protein / 0.718
2j7p GNPSignal recognition particle receptor FtsY / 0.718
1t91 GTPRas-related protein Rab-7a / 0.717
1vg8 GNPRas-related protein Rab-7a / 0.717
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.717
1svm ATPLarge T antigen 3.6.4 0.716
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.716
1yzq GNPRas-related protein Rab-6A / 0.715
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.715
3tjz GNPADP-ribosylation factor 1 / 0.715
4db1 ANPMyosin-7 / 0.715
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.713
4d0l GSPRas-related protein Rab-11A / 0.713
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.713
3r9x GNPGTPase Era / 0.712
4dsn GCPGTPase KRas / 0.712
4nh0 ATPESX secretion system protein EccC / 0.712
4luc GDPGTPase KRas / 0.711
1fmw ATPMyosin-2 heavy chain / 0.709
4idp GNPAtlastin-1 3.6.5 0.709
3tnf GNPRas-related protein Rab-8A / 0.707
3zfd ANPChromosome-associated kinesin KIF4 / 0.707
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.706
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.706
4k81 GTPGTPase HRas / 0.706
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.706
1sdm ADPKinesin heavy chain-like protein / 0.705
1uad GNPRas-related protein Ral-A / 0.705
1tu3 GNPRas-related protein Rab-5A / 0.704
4c2u ANPDNA helicase / 0.704
2gcp GSPRho-related GTP-binding protein RhoC / 0.703
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.702
4dvg GSPRho family GTPase / 0.702
3law GNPRas-related protein Rab-7a / 0.701
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.701
3eg5 GNPCell division control protein 42 homolog / 0.700
4kvg GTPRas-related protein Rap-1A / 0.700
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.699
2y65 ADPKinesin heavy chain / 0.698
1s1c GNPTransforming protein RhoA / 0.697
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.696
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.696
2xtn GTPGTPase IMAP family member 2 / 0.696
4v02 ATPSite-determining protein / 0.696
1lfd GNPGTPase HRas / 0.695
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.694
4ihq ADPConserved Archaeal protein / 0.694
1sxj AGSReplication factor C subunit 1 / 0.691
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.691
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.690
1svl ADPLarge T antigen 3.6.4 0.690
1z2a GDPRas-related protein Rab-23 / 0.690
4gp6 ADPMetallophosphoesterase / 0.690
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.689
5di3 GNPADP-ribosylation factor-like protein 3 / 0.689
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.688
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
1am4 GNPCell division control protein 42 homolog / 0.687
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.686
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.685
4ohv ANPProtein clpf-1 / 0.683
4nu0 AP5Adenylate kinase / 0.682
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.681
2zet GTPRas-related protein Rab-27B / 0.681
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.681
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.680
1rrg GDPADP-ribosylation factor 1 / 0.679
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.679
4tyq AP5Adenylate kinase / 0.678
1xp8 AGSProtein RecA / 0.677
2zts ADPUncharacterized protein / 0.676
1oe0 TTPDeoxynucleoside kinase / 0.675
1w5t ANPORC1-type DNA replication protein 2 / 0.674
1xts GTPGTP-binding protein Rheb / 0.674
2cl6 CAGGTPase HRas / 0.674
3vhx GTPADP-ribosylation factor 6 / 0.674
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.673
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.673
1rj9 GCPSignal recognition particle receptor FtsY / 0.673
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.672
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.672
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.671
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
1mmg AGSMyosin-2 heavy chain / 0.671
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.671
3hqd ANPKinesin-like protein KIF11 / 0.670
4qnr ATPPsp operon transcriptional activator / 0.670
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.669
5i4n ATPTyrosine-protein kinase JAK2 / 0.669
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.668
5l3s GNPSignal recognition particle receptor FtsY / 0.668
4aff ATPNitrogen regulatory protein P-II / 0.667
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.665
1pox TPPPyruvate oxidase 1.2.3.3 0.664
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.664
4lv8 ADPRhoptry protein 5 C / 0.664
1d5c GDPGTPase (Rab6) / 0.663
1nsf ATPVesicle-fusing ATPase 3.6.4.6 0.663
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.663
4l8g GDPGTPase KRas / 0.663
3kkq GDPRas-related protein M-Ras / 0.662
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.662
4epx GDPGTPase KRas / 0.662
2pui ADPMethylthioribose kinase 2.7.1.100 0.661
4iij GTPTubulin alpha-1B chain / 0.661
4qbg AP5Adenylate kinase / 0.661
2pyw ADPMethylthioribose kinase 2.7.1.100 0.660
5itz GTPTubulin alpha-1B chain / 0.660
4dee ADPAurora kinase A 2.7.11.1 0.659
3krf DSTGeranyl diphosphate synthase large subunit / 0.658
5da9 AGSUncharacterized protein / 0.657
1p3j AP5Adenylate kinase / 0.656
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.656
3q9l ATPSeptum site-determining protein MinD / 0.656
3ruq ADPChaperonin / 0.656
4c30 ANPDNA helicase / 0.656
4fvq ATPTyrosine-protein kinase JAK2 / 0.656
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.655
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.655
2a92 NAIL-lactate dehydrogenase / 0.653
2l0x GDPGTP-binding protein Rheb / 0.653
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.653
1pow TPPPyruvate oxidase 1.2.3.3 0.652
2fg5 GNPRas-related protein Rab-31 / 0.652
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.652
2zxu DSTtRNA dimethylallyltransferase 2.5.1.75 0.652
3a58 GNPGTP-binding protein RHO1 / 0.652
2j40 NAD1-pyrroline-5-carboxylate dehydrogenase / 0.651
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.651
3nbz GTPGTP-binding nuclear protein Ran / 0.651
4ffb GTPTubulin alpha-1 chain / 0.651
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.650
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.650
4o4l GTPTubulin alpha-1B chain / 0.650
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.650
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.650