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
1svm ATP Large T antigen 3.6.4

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1svm ATPLarge T antigen 3.6.4 1.237
1svl ADPLarge T antigen 3.6.4 0.859
4qm6 GTPMetallophosphoesterase / 0.811
4jsy GTPMetallophosphoesterase / 0.810
4nu0 AP5Adenylate kinase / 0.793
2aky AP5Adenylate kinase / 0.790
3wyf GTPGTP-binding nuclear protein / 0.790
3vhx GTPADP-ribosylation factor 6 / 0.789
2ffq GSPRas-related protein Rab-6B / 0.786
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.777
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.775
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.775
1p3j AP5Adenylate kinase / 0.775
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.774
4w5j AP5Adenylate kinase / 0.773
4mkg AP5Adenylate kinase / 0.772
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.771
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.766
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.762
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.762
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.762
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.761
3mjh GTPRas-related protein Rab-5A / 0.761
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.759
3dkv AP5Adenylate kinase / 0.758
3w3z GTPGTP-binding nuclear protein Ran / 0.758
4dso GSPGTPase KRas / 0.758
1gwn GTPRho-related GTP-binding protein RhoE / 0.757
4xsg GSPTransforming protein RhoA / 0.757
3tkl GTPRas-related protein Rab-1A / 0.756
2eu8 AP5Adenylate kinase / 0.755
4xoi GTPTransforming protein RhoA / 0.755
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.754
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.752
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.751
2qaj AP5Adenylate kinase / 0.751
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.750
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.746
2oo7 AP5Adenylate kinase / 0.745
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.745
2bku GTPGTP-binding nuclear protein Ran / 0.744
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.744
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.744
2gcp GSPRho-related GTP-binding protein RhoC / 0.742
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.741
1a2b GSPTransforming protein RhoA / 0.740
1m7b GTPRho-related GTP-binding protein RhoE / 0.740
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.739
1mmg AGSMyosin-2 heavy chain / 0.739
1v8k ANPKinesin-like protein KIF2C / 0.739
2c5l GTPGTPase HRas / 0.739
1z0d GDPRas-related protein Rab-5C / 0.737
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.737
4js0 GNPCell division control protein 42 homolog / 0.735
4tyq AP5Adenylate kinase / 0.735
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.733
1cxz GSPTransforming protein RhoA / 0.732
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.732
2osb AP5Adenylate kinase / 0.732
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.732
4mkf AP5Adenylate kinase / 0.732
4nyj GNPGTPase HRas / 0.732
1t91 GTPRas-related protein Rab-7a / 0.728
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.728
3m0e ATPTranscriptional regulator (NtrC family) / 0.727
1zc4 GNPRas-related protein Ral-A / 0.726
4dxa GSPRas-related protein Rap-1b / 0.726
3law GNPRas-related protein Rab-7a / 0.725
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.724
4g0n GNPGTPase HRas / 0.722
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.721
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.721
4kvg GTPRas-related protein Rap-1A / 0.721
1b7t ADPMyosin heavy chain, striated muscle / 0.720
1s1c GNPTransforming protein RhoA / 0.720
2qen ADPWalker-Type ATPase / 0.720
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.719
3tnf GNPRas-related protein Rab-8A / 0.719
2uyi ADPKinesin-like protein KIF11 / 0.718
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.718
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.718
1fnn ADPORC1-type DNA replication protein / 0.716
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.716
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.716
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.715
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.715
1d5c GDPGTPase (Rab6) / 0.715
2fe4 GDPRas-related protein Rab-6B / 0.715
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.714
3myk ANPMyosin-2 heavy chain / 0.714
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.714
5di3 GNPADP-ribosylation factor-like protein 3 / 0.714
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.713
3e5h GNPRas-related protein Rab-28 / 0.712
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.711
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.711
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.710
2x7e ADPKinesin-like protein KIF11 / 0.710
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.710
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.710
4qxa GTPRas-related protein Rab-9A / 0.710
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.709
1vg8 GNPRas-related protein Rab-7a / 0.709
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.709
4g01 GDPRas-related protein RABF2b / 0.709
2rge GNPGTPase HRas / 0.708
3lbn GNPGTPase HRas / 0.708
5dac AGSUncharacterized protein / 0.708
1tu3 GNPRas-related protein Rab-5A / 0.707
2pg2 ADPKinesin-like protein KIF11 / 0.707
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.707
3bbp GTPRas-related protein Rab-6A / 0.707
3rsl GNPGTPase HRas / 0.707
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.707
1xp8 AGSProtein RecA / 0.706
3l9h ADPKinesin-like protein KIF11 / 0.704
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.704
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.704
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.703
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.703
4nh0 ATPESX secretion system protein EccC / 0.703
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.702
4l8g GDPGTPase KRas / 0.702
2cls GTPRho-related GTP-binding protein Rho6 / 0.701
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.701
3kz1 GSPTransforming protein RhoA / 0.701
4dzz ADPPlasmid partitioning protein ParF / 0.701
2dr3 ADPUPF0273 protein PH0284 / 0.700
3rab GNPRas-related protein Rab-3A / 0.700
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.699
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.699
2hld ANPATP synthase subunit alpha, mitochondrial / 0.698
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
3oiw GNPGTPase HRas / 0.698
3rs0 GNPGTPase HRas / 0.698
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.698
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.697
4mit GTPRho-related protein racC / 0.697
4xvu ATPATPase GET3 / 0.697
1sxj AGSReplication factor C subunit 1 / 0.696
1zbd GTPRas-related protein Rab-3A / 0.696
3oiu GNPGTPase HRas / 0.696
1kmq GNPTransforming protein RhoA / 0.695
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.695
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.695
1xmv ADPProtein RecA / 0.695
3v4f GNPGTPase HRas / 0.695
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.694
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.694
4lv6 GDPGTPase KRas / 0.694
5dha GNPGTP-binding nuclear protein Ran / 0.694
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.693
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.693
4dls GNPGTPase HRas / 0.693
1w5t ANPORC1-type DNA replication protein 2 / 0.692
1wa5 GTPGTP-binding nuclear protein Ran / 0.692
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.692
3i3s GNPGTPase HRas / 0.692
3k8y GNPGTPase HRas / 0.692
1g17 GNPRas-related protein SEC4 / 0.691
2whx ADPGenome polyprotein 3.4.21.91 0.691
3rs4 GNPGTPase HRas / 0.691
3rs7 GNPGTPase HRas / 0.691
5b2z GNPGTPase HRas / 0.691
2rgb GNPGTPase HRas / 0.690
3ddc GNPGTPase HRas / 0.690
4dlt GNPGTPase HRas / 0.690
4dlv GNPGTPase HRas / 0.690
4h5c YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.690
4nyi GNPGTPase HRas / 0.690
2rgc GNPGTPase HRas / 0.689
3tgp GNPGTPase HRas / 0.689
4o2l GTPGTP-binding protein Rheb / 0.689
1w5t ADPORC1-type DNA replication protein 2 / 0.688
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.688
4dlw GNPGTPase HRas / 0.688
4dlx GNPGTPase HRas / 0.688
1yzq GNPRas-related protein Rab-6A / 0.687
3kkq GDPRas-related protein M-Ras / 0.687
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.686
3nbz GTPGTP-binding nuclear protein Ran / 0.686
4dvg GSPRho family GTPase / 0.686
4v02 ATPSite-determining protein / 0.686
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.685
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.685
1yrs ADPKinesin-like protein KIF11 / 0.684
2fg5 GNPRas-related protein Rab-31 / 0.684
3ieu GDPGTPase Era / 0.684
4cym GCPRas-related protein Rab-32 / 0.684
4idn GNPAtlastin-1 3.6.5 0.684
5i4n ATPTyrosine-protein kinase JAK2 / 0.684
3c41 ANPAmino acid ABC transporter / 0.683
3pcr GTPADP-ribosylation factor 6 / 0.682
4o2r GDPGTP-binding protein Rheb / 0.682
2vor ACPFolylpolyglutamate synthase / 0.681
2xsz ATPRuvB-like 2 3.6.4.12 0.681
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.681
3k1j ADPATP-dependent protease Lon / 0.681
4rkf GNPRas-related protein Rab-3 / 0.681
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.679
2gil GTPRas-related protein Rab-6A / 0.677
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.677
4fvq ATPTyrosine-protein kinase JAK2 / 0.677
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
4c2u ANPDNA helicase / 0.676
4q23 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.676
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.674
3pit GNPRas-related protein M-Ras / 0.674
4lhw GNPRas-related protein Rab-8A / 0.674
1k5d GNPGTP-binding nuclear protein Ran / 0.673
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.672
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
3kud GDPGTPase HRas / 0.672
3l8y GNPGTPase HRas / 0.672
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.672
4l9w GNPGTPase HRas / 0.672
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.671
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
1zw5 ZOLFarnesyl pyrophosphate synthase 2.5.1.10 0.671
4xvq GNPGTPase HRas / 0.671
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.670
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.669
4fvr ATPTyrosine-protein kinase JAK2 / 0.669
2bc9 GNPGuanylate-binding protein 1 / 0.668
2x19 GTPGTP-binding nuclear protein GSP1/CNR1 / 0.668
3kko GNPRas-related protein M-Ras / 0.668
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.668
4dsn GCPGTPase KRas / 0.668
4mkh AP5Adenylate kinase / 0.668
3kuc GDPRas-related protein Rap-1A / 0.667
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.667
2fl2 ADPKinesin-like protein KIF11 / 0.666
3ldw ZOLFarnesyl pyrophosphate synthase, putative / 0.665
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.665
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.664
3lbh GNPGTPase HRas / 0.664
3zcb ATPAdenosine monophosphate-protein transferase VbhT 2.7.7.n1 0.664
4cid ANPEH domain-containing protein 2 / 0.664
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.663
2w02 ATPAcsD / 0.663
3dyh 721Farnesyl pyrophosphate synthase / 0.663
1ii6 ADPKinesin-like protein KIF11 / 0.662
1zm7 TTPDeoxynucleoside kinase / 0.662
3dl0 AP5Adenylate kinase / 0.662
3ftq GNPSeptin-2 / 0.662
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.661
2xtn GTPGTPase IMAP family member 2 / 0.661
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.661
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.661
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.660
2gm1 ADPKinesin-like protein KIF11 / 0.657
2r9v ATPATP synthase subunit alpha / 0.657
3q5d GDPAtlastin-1 3.6.5 0.657
4ptf DCPDNA polymerase epsilon catalytic subunit A 2.7.7.7 0.657
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.657
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.656
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.656
4asu ADPATP synthase subunit alpha, mitochondrial / 0.656
4i1v ADPDephospho-CoA kinase / 0.656
1yra GDPGPN-loop GTPase PAB0955 / 0.655
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.655
4jky ADPAdenylate kinase / 0.655
2ql6 ADPNicotinamide riboside kinase 1 / 0.654
3lbi GNPGTPase HRas / 0.653
3rs5 GNPGTPase HRas / 0.653
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.652
3ea5 GDPGTP-binding nuclear protein Ran / 0.651
3hqd ANPKinesin-like protein KIF11 / 0.651
3q9l ATPSeptum site-determining protein MinD / 0.651
2bbw GP5Adenylate kinase 4, mitochondrial / 0.650
2zet GTPRas-related protein Rab-27B / 0.650
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.650
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.650
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.650
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.650