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
4bec ATP Type I restriction enzyme EcoR124II R protein 3.1.21.3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 1.118
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.969
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.912
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.818
2bc9 GNPGuanylate-binding protein 1 / 0.782
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.776
3q9l ATPSeptum site-determining protein MinD / 0.773
2jlr ANPGenome polyprotein 3.4.21.91 0.768
4idn GNPAtlastin-1 3.6.5 0.765
4qm6 GTPMetallophosphoesterase / 0.765
3pit GNPRas-related protein M-Ras / 0.756
4c2u ANPDNA helicase / 0.756
3m0e ATPTranscriptional regulator (NtrC family) / 0.749
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.748
4dlv GNPGTPase HRas / 0.747
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.745
3ftq GNPSeptin-2 / 0.745
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.743
3kko GNPRas-related protein M-Ras / 0.743
4lhw GNPRas-related protein Rab-8A / 0.743
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.743
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.742
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.742
3i3s GNPGTPase HRas / 0.742
3k8y GNPGTPase HRas / 0.742
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.741
3tgp GNPGTPase HRas / 0.741
3fkq ATPNtrC-like two-domain protein / 0.740
1kmq GNPTransforming protein RhoA / 0.738
5l3s GNPSignal recognition particle receptor FtsY / 0.738
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.737
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.737
1z2c GNPRho-related GTP-binding protein RhoC / 0.736
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.735
3tso GNPRas-related protein Rab-25 / 0.732
1zc3 GNPRas-related protein Ral-A / 0.731
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.731
3rab GNPRas-related protein Rab-3A / 0.730
4xoi GTPTransforming protein RhoA / 0.729
3qbt GNPRas-related protein Rab-8A / 0.728
4xvu ATPATPase GET3 / 0.728
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.727
1s1c GNPTransforming protein RhoA / 0.727
1zc4 GNPRas-related protein Ral-A / 0.727
3oes GNPGTPase RhebL1 / 0.727
3a58 GNPGTP-binding protein RHO1 / 0.725
1esn ANPPantothenate kinase 2.7.1.33 0.724
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.724
3ddc GNPGTPase HRas / 0.724
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.724
1ky2 GNPGTP-binding protein YPT7 / 0.723
1n6l GTPRas-related protein Rab-5A / 0.723
3k9l GNPGTPase HRas / 0.723
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.722
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.722
1f5n GNPGuanylate-binding protein 1 / 0.722
1xtr GNPGTP-binding protein Rheb / 0.722
4c30 ANPDNA helicase / 0.722
4g0n GNPGTPase HRas / 0.722
1yzq GNPRas-related protein Rab-6A / 0.721
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.721
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.721
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.720
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.720
1ank ANPAdenylate kinase / 0.719
1yu9 GNPRas-related protein Rab-4A / 0.719
3l8y GNPGTPase HRas / 0.719
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.718
4idp GNPAtlastin-1 3.6.5 0.718
1nsf ATPVesicle-fusing ATPase 3.6.4.6 0.717
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.717
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.717
4db1 ANPMyosin-7 / 0.716
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.715
1w5t ANPORC1-type DNA replication protein 2 / 0.714
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.714
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.714
2rge GNPGTPase HRas / 0.711
2rgg GNPGTPase HRas / 0.711
3zfd ANPChromosome-associated kinesin KIF4 / 0.711
4nh0 ATPESX secretion system protein EccC / 0.711
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.710
2bme GNPRas-related protein Rab-4A / 0.709
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.709
1cxz GSPTransforming protein RhoA / 0.708
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.708
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.708
2j7p GNPSignal recognition particle protein / 0.708
2j7p GNPSignal recognition particle receptor FtsY / 0.708
3oiv GNPGTPase HRas / 0.708
5dif GNPGTP-binding nuclear protein Ran / 0.708
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.708
1vg8 GNPRas-related protein Rab-7a / 0.707
3lbh GNPGTPase HRas / 0.707
1am4 GNPCell division control protein 42 homolog / 0.705
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.705
3c41 ANPAmino acid ABC transporter / 0.705
2cl6 CAGGTPase HRas / 0.704
4mkf AP5Adenylate kinase / 0.704
4v02 ATPSite-determining protein / 0.704
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.703
3rs0 GNPGTPase HRas / 0.703
1t91 GTPRas-related protein Rab-7a / 0.702
5di3 GNPADP-ribosylation factor-like protein 3 / 0.701
3zia ATPATP synthase subunit alpha, mitochondrial / 0.700
4z54 GDPNeuronal-specific septin-3 / 0.700
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.699
2r9v ATPATP synthase subunit alpha / 0.699
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.699
3mjh GTPRas-related protein Rab-5A / 0.699
1fmw ATPMyosin-2 heavy chain / 0.698
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.698
3oee ANPATP synthase subunit alpha, mitochondrial / 0.698
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
4js0 GNPCell division control protein 42 homolog / 0.698
4jsy GTPMetallophosphoesterase / 0.698
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.697
4gp6 ADPMetallophosphoesterase / 0.697
4ohv ANPProtein clpf-1 / 0.697
1mmg AGSMyosin-2 heavy chain / 0.695
1rj9 GCPSignal recognition particle receptor FtsY / 0.695
3oiu GNPGTPase HRas / 0.695
4cf7 ADPAdenylate kinase / 0.695
5dha GNPGTP-binding nuclear protein Ran / 0.695
5k5z ANPUncharacterized protein / 0.695
2j5x GSPADP-ribosylation factor 6 / 0.694
3rs5 GNPGTPase HRas / 0.694
5b2z GNPGTPase HRas / 0.694
2q3f GNPRas-related GTP-binding protein D / 0.693
3myk ANPMyosin-2 heavy chain / 0.693
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.692
2hld ANPATP synthase subunit alpha, mitochondrial / 0.692
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.692
4dso GSPGTPase KRas / 0.692
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.692
4qxa GTPRas-related protein Rab-9A / 0.692
4xvq GNPGTPase HRas / 0.692
1gwn GTPRho-related GTP-binding protein RhoE / 0.690
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.690
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.690
3tnf GNPRas-related protein Rab-8A / 0.690
4goj GNPADP-ribosylation factor-like protein 3 / 0.689
1uad GNPRas-related protein Ral-A / 0.687
1m7b GTPRho-related GTP-binding protein RhoE / 0.686
1tu3 GNPRas-related protein Rab-5A / 0.686
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.686
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.686
3b1x GNPFerrous iron transport protein B / 0.686
3wyf GTPGTP-binding nuclear protein / 0.686
4dsn GCPGTPase KRas / 0.686
4lhv GDPRas-related protein Rab-8A / 0.686
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.684
4rkf GNPRas-related protein Rab-3 / 0.684
5c46 GSPRas-related protein Rab-11A / 0.684
4xsg GSPTransforming protein RhoA / 0.683
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.682
2c96 ATPPsp operon transcriptional activator / 0.682
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.681
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
1rrg GDPADP-ribosylation factor 1 / 0.681
1wdt GTPElongation factor G (EF-G-2) / 0.681
3v4f GNPGTPase HRas / 0.681
4pfp ADPUnconventional myosin-VI / 0.681
4pjj ADPUnconventional myosin-VI / 0.681
1jx2 ADPMyosin-2 heavy chain / 0.680
2gcp GSPRho-related GTP-binding protein RhoC / 0.680
4hdo GNPRas-related protein Rap-1b / 0.680
4o25 GTPGTP-binding protein Rheb / 0.680
1a2b GSPTransforming protein RhoA / 0.679
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.679
3rs4 GNPGTPase HRas / 0.679
4dlx GNPGTPase HRas / 0.679
4dlz GNPGTPase HRas / 0.679
2ffq GSPRas-related protein Rab-6B / 0.678
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.678
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.678
5jlj GNPGTP-binding nuclear protein Ran / 0.678
2gil GTPRas-related protein Rab-6A / 0.677
4yqf GDPSeptin-9 / 0.677
1wa5 GTPGTP-binding nuclear protein Ran / 0.676
3x1z GNPRas-related protein Rap-1b / 0.676
4dls GNPGTPase HRas / 0.676
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.675
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.674
3rsl GNPGTPase HRas / 0.674
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.674
4qos ADPPsp operon transcriptional activator / 0.674
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.673
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.673
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.672
1nbm ATPATP synthase subunit alpha, mitochondrial / 0.672
2q0c CTPPoly(A) polymerase, putative / 0.672
3oiw GNPGTPase HRas / 0.672
3vhx GTPADP-ribosylation factor 6 / 0.672
4o2l GTPGTP-binding protein Rheb / 0.672
4q03 GDPGTPase KRas / 0.672
4qnr ATPPsp operon transcriptional activator / 0.672
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.671
1z0a GDPRas-related protein Rab-2A / 0.670
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.670
2gm1 ADPKinesin-like protein KIF11 / 0.670
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.669
4hdq GNPRas-related protein Rap-1b / 0.669
4kvg GTPRas-related protein Rap-1A / 0.669
4o3m ADPBloom syndrome protein 3.6.4.12 0.669
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.669
4ys0 ADPProtein translocase subunit SecA / 0.669
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.668
2fg5 GNPRas-related protein Rab-31 / 0.668
4epx GDPGTPase KRas / 0.668
4pk4 ADPUnconventional myosin-VI / 0.668
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.667
3dl0 AP5Adenylate kinase / 0.667
1oix GDPRas-related protein Rab-11A / 0.666
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.666
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.666
3rs7 GNPGTPase HRas / 0.666
1mma ADPMyosin-2 heavy chain / 0.665
2c5l GTPGTPase HRas / 0.665
3w3z GTPGTP-binding nuclear protein Ran / 0.665
1zm7 TTPDeoxynucleoside kinase / 0.664
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.664
3kuc GDPRas-related protein Rap-1A / 0.664
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
4cid ANPEH domain-containing protein 2 / 0.664
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.663
1sq5 ADPPantothenate kinase 2.7.1.33 0.663
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.663
3tqc ADPPantothenate kinase / 0.663
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.662
4q02 GDPGTPase KRas / 0.661
2bbw GP5Adenylate kinase 4, mitochondrial / 0.660
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.660
3tjz GNPADP-ribosylation factor 1 / 0.660
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
2npi ATPmRNA cleavage and polyadenylation factor CLP1 / 0.659
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.659
3ea5 GDPGTP-binding nuclear protein Ran / 0.658
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.658
4rz3 ADPSite-determining protein / 0.658
5da9 AGSUncharacterized protein / 0.658
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.657
3x1w GDPRas-related protein Rap-1b / 0.657
4zgn ATPCell division cycle protein 123 / 0.657
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.657
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.656
1dvr ATFAdenylate kinase / 0.656
3eg5 GNPCell division control protein 42 homolog / 0.656
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.656
4jl5 ADPAdenylate kinase / 0.656
2q0d ATPPoly(A) polymerase, putative / 0.655
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.655
4jjz ADPFormate--tetrahydrofolate ligase / 0.655
4l9w GNPGTPase HRas / 0.655
4nyj GNPGTPase HRas / 0.655
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.654
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.654
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.653
4dlt GNPGTPase HRas / 0.653
4dlw GNPGTPase HRas / 0.653
4ldj GDPGTPase KRas / 0.653
4pjk ADPMyosin-2 heavy chain / 0.653
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.653
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.652
2rgb GNPGTPase HRas / 0.652
4ihq ADPConserved Archaeal protein / 0.652
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.651
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.650