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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
4c2u ANP DNA helicase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4c2u ANPDNA helicase / 1.264
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.907
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.845
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.842
4dlz GNPGTPase HRas / 0.831
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.831
4dsn GCPGTPase KRas / 0.827
3kko GNPRas-related protein M-Ras / 0.818
4idp GNPAtlastin-1 3.6.5 0.816
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.813
4c30 ANPDNA helicase / 0.805
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.800
1yzq GNPRas-related protein Rab-6A / 0.799
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.797
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.795
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.795
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.794
1zc4 GNPRas-related protein Ral-A / 0.794
1tu3 GNPRas-related protein Rab-5A / 0.791
1wdt GTPElongation factor G (EF-G-2) / 0.790
4dxa GSPRas-related protein Rap-1b / 0.788
2rgc GNPGTPase HRas / 0.787
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.783
4lhw GNPRas-related protein Rab-8A / 0.783
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.778
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.778
5k5z ANPUncharacterized protein / 0.777
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.774
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.774
1zc3 GNPRas-related protein Ral-A / 0.772
2jlr ANPGenome polyprotein 3.4.21.91 0.769
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.767
3tkl GTPRas-related protein Rab-1A / 0.767
4cid ANPEH domain-containing protein 2 / 0.767
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.765
4xvr GNPGTPase HRas / 0.763
1w5s ADPORC1-type DNA replication protein 2 / 0.761
1lfd GNPGTPase HRas / 0.760
1g17 GNPRas-related protein SEC4 / 0.757
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.756
1z0d GDPRas-related protein Rab-5C / 0.755
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.755
2j5x GSPADP-ribosylation factor 6 / 0.755
4nyi GNPGTPase HRas / 0.753
2osb AP5Adenylate kinase / 0.752
4asu ADPATP synthase subunit alpha, mitochondrial / 0.752
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.749
3k9l GNPGTPase HRas / 0.749
3tnf GNPRas-related protein Rab-8A / 0.749
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.747
4jlo ADPAdenylate kinase / 0.747
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.746
4jl5 ADPAdenylate kinase / 0.744
4v02 ATPSite-determining protein / 0.744
2c9c ATPPsp operon transcriptional activator / 0.743
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.743
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.743
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.742
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.741
4nh0 ATPESX secretion system protein EccC / 0.740
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.739
2cl6 CAGGTPase HRas / 0.738
5di3 GNPADP-ribosylation factor-like protein 3 / 0.736
1oix GDPRas-related protein Rab-11A / 0.734
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.734
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.734
3tqc ADPPantothenate kinase / 0.733
4qos ADPPsp operon transcriptional activator / 0.732
3i3s GNPGTPase HRas / 0.730
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.729
1z0a GDPRas-related protein Rab-2A / 0.728
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.726
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.726
4q02 GDPGTPase KRas / 0.726
4lv6 GDPGTPase KRas / 0.724
4nyj GNPGTPase HRas / 0.724
1fmw ATPMyosin-2 heavy chain / 0.722
4d0l GSPRas-related protein Rab-11A / 0.722
1a2b GSPTransforming protein RhoA / 0.721
4jky ADPAdenylate kinase / 0.721
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.720
4itr GDPCell division control protein 42 homolog / 0.720
4tyq AP5Adenylate kinase / 0.719
1d5c GDPGTPase (Rab6) / 0.718
1wbb ADPDNA mismatch repair protein MutS / 0.718
1zbd GTPRas-related protein Rab-3A / 0.718
4hse ADPChaperone protein ClpB / 0.716
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.715
1fnn ADPORC1-type DNA replication protein / 0.713
2eck ADPAdenylate kinase / 0.710
3c41 ANPAmino acid ABC transporter / 0.709
4wa7 GDPGTPase KRas / 0.709
4luc GDPGTPase KRas / 0.708
2zet GTPRas-related protein Rab-27B / 0.706
4uj3 GNPRas-related protein Rab-11A / 0.706
1w5t ADPORC1-type DNA replication protein 2 / 0.704
3e5h GNPRas-related protein Rab-28 / 0.704
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.704
4ol0 GTPGTP-binding nuclear protein Ran / 0.704
1p9w ANPType II secretion system protein E / 0.702
2c96 ATPPsp operon transcriptional activator / 0.702
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.702
3bbp GTPRas-related protein Rab-6A / 0.702
3ftq GNPSeptin-2 / 0.701
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.701
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.699
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.698
4jl6 ADPAdenylate kinase / 0.698
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.696
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.695
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.694
4l9s GDPGTPase HRas / 0.693
3d8b ADPFidgetin-like protein 1 3.6.4 0.692
3ddc GNPGTPase HRas / 0.692
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.691
2hld ANPATP synthase subunit alpha, mitochondrial / 0.691
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.691
3cph GDPRas-related protein SEC4 / 0.691
1w5t ANPORC1-type DNA replication protein 2 / 0.690
3m0e ATPTranscriptional regulator (NtrC family) / 0.690
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.690
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.689
1ny5 ADPTranscriptional regulator (NtrC family) / 0.688
2bbw GP5Adenylate kinase 4, mitochondrial / 0.688
4epx GDPGTPase KRas / 0.688
1esn ANPPantothenate kinase 2.7.1.33 0.686
2rgx AP5Adenylate kinase / 0.685
3lbh GNPGTPase HRas / 0.684
1xms ANPProtein RecA / 0.683
4o25 GTPGTP-binding protein Rheb / 0.682
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.680
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.680
4js0 GNPCell division control protein 42 homolog / 0.680
1ank ANPAdenylate kinase / 0.678
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.678
3ump ATPATP-dependent 6-phosphofructokinase isozyme 2 2.7.1.11 0.678
1svm ATPLarge T antigen 3.6.4 0.676
1xts GTPGTP-binding protein Rheb / 0.676
3zoz ADPPhosphoglycerate kinase 1 2.7.2.3 0.674
4iei ADPGene 2 protein / 0.672
2ql6 ADPNicotinamide riboside kinase 1 / 0.671
1z2c GNPRho-related GTP-binding protein RhoC / 0.670
4o2l GTPGTP-binding protein Rheb / 0.670
4qnr ATPPsp operon transcriptional activator / 0.669
4rz3 ADPSite-determining protein / 0.669
2r6g ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.668
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.667
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.666
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.665
1dvr ATFAdenylate kinase / 0.664
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.664
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.664
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
1oe0 TTPDeoxynucleoside kinase / 0.663
2vp0 TTPDeoxynucleoside kinase / 0.662
3umo ATPATP-dependent 6-phosphofructokinase isozyme 2 2.7.1.11 0.662
4qbh AP5Adenylate kinase / 0.662
1svw GTPProbable GTP-binding protein EngB / 0.661
2l0x GDPGTP-binding protein Rheb / 0.661
4xsg GSPTransforming protein RhoA / 0.661
3n0z 3ATAdenylate cyclase 2 / 0.659
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
2x0q ATPAlcaligin biosynthesis protein / 0.658
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.658
3tlx ADPAdenylate kinase 2 / 0.658
4l16 ADPFidgetin-like protein 1 3.6.4 0.658
3r9i ADPSeptum site-determining protein MinD / 0.657
1z6t ADPApoptotic protease-activating factor 1 / 0.656
3oiw GNPGTPase HRas / 0.656
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.656
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.656
1a4r GNHCell division control protein 42 homolog / 0.654
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.654
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.654
1kmq GNPTransforming protein RhoA / 0.653
5l3s GNPSignal recognition particle receptor FtsY / 0.653
3oiv GNPGTPase HRas / 0.652
4q72 FADBifunctional protein PutA / 0.652
3oiu GNPGTPase HRas / 0.651
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.650
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.650
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.650