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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
4xjx 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
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 1.261
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.969
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.964
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.899
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.884
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.871
4xvu ATPATPase GET3 / 0.824
3rab GNPRas-related protein Rab-3A / 0.822
5l3s GNPSignal recognition particle receptor FtsY / 0.818
4beb ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.817
4idp GNPAtlastin-1 3.6.5 0.816
1zc4 GNPRas-related protein Ral-A / 0.810
4dso GSPGTPase KRas / 0.799
4c2u ANPDNA helicase / 0.797
3rs4 GNPGTPase HRas / 0.795
3rs7 GNPGTPase HRas / 0.795
4dlt GNPGTPase HRas / 0.795
4dlv GNPGTPase HRas / 0.795
3pit GNPRas-related protein M-Ras / 0.794
3rs5 GNPGTPase HRas / 0.794
4dlx GNPGTPase HRas / 0.794
3rs0 GNPGTPase HRas / 0.793
4dlz GNPGTPase HRas / 0.793
4nyj GNPGTPase HRas / 0.793
4idn GNPAtlastin-1 3.6.5 0.792
4l9w GNPGTPase HRas / 0.792
3l8y GNPGTPase HRas / 0.787
5dha GNPGTP-binding nuclear protein Ran / 0.785
1gwn GTPRho-related GTP-binding protein RhoE / 0.783
2j7p GNPSignal recognition particle protein / 0.782
2j7p GNPSignal recognition particle receptor FtsY / 0.782
3kko GNPRas-related protein M-Ras / 0.782
1wdt GTPElongation factor G (EF-G-2) / 0.780
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.780
3i3s GNPGTPase HRas / 0.780
3k8y GNPGTPase HRas / 0.780
3rsl GNPGTPase HRas / 0.780
2rge GNPGTPase HRas / 0.779
3ddc GNPGTPase HRas / 0.779
3oiw GNPGTPase HRas / 0.779
3x1z GNPRas-related protein Rap-1b / 0.779
4xvq GNPGTPase HRas / 0.779
2r9v ATPATP synthase subunit alpha / 0.778
3lbh GNPGTPase HRas / 0.778
3oiv GNPGTPase HRas / 0.778
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.778
3lbi GNPGTPase HRas / 0.776
4hdo GNPRas-related protein Rap-1b / 0.776
4lhw GNPRas-related protein Rab-8A / 0.776
3lbn GNPGTPase HRas / 0.775
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.774
2jlr ANPGenome polyprotein 3.4.21.91 0.774
2rgg GNPGTPase HRas / 0.774
2cl6 CAGGTPase HRas / 0.773
2rgc GNPGTPase HRas / 0.773
3ftq GNPSeptin-2 / 0.771
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.768
5dif GNPGTP-binding nuclear protein Ran / 0.768
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.766
3fkq ATPNtrC-like two-domain protein / 0.766
4js0 GNPCell division control protein 42 homolog / 0.764
4ohv ANPProtein clpf-1 / 0.764
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.762
1n6l GTPRas-related protein Rab-5A / 0.761
3tso GNPRas-related protein Rab-25 / 0.761
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.761
1vg8 GNPRas-related protein Rab-7a / 0.760
1yu9 GNPRas-related protein Rab-4A / 0.760
3bc1 GNPRas-related protein Rab-27A / 0.760
1g17 GNPRas-related protein SEC4 / 0.759
2ffq GSPRas-related protein Rab-6B / 0.759
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.758
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.758
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.758
3k9l GNPGTPase HRas / 0.758
4kvg GTPRas-related protein Rap-1A / 0.758
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.758
3b1x GNPFerrous iron transport protein B / 0.756
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.755
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.755
4goj GNPADP-ribosylation factor-like protein 3 / 0.755
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.753
3mjh GTPRas-related protein Rab-5A / 0.751
4nyi GNPGTPase HRas / 0.751
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.749
4qxa GTPRas-related protein Rab-9A / 0.749
4uj3 GNPRas-related protein Rab-11A / 0.749
4z54 GDPNeuronal-specific septin-3 / 0.746
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.744
4dls GNPGTPase HRas / 0.744
1m7b GTPRho-related GTP-binding protein RhoE / 0.743
1wa5 GTPGTP-binding nuclear protein Ran / 0.743
4k81 GTPGTPase HRas / 0.743
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.740
1fmw ATPMyosin-2 heavy chain / 0.739
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.739
4tyq AP5Adenylate kinase / 0.739
4xvr GNPGTPase HRas / 0.739
1zbd GTPRas-related protein Rab-3A / 0.738
3oes GNPGTPase RhebL1 / 0.738
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.737
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.736
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.736
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.735
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.734
4l9s GDPGTPase HRas / 0.733
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.733
4ql3 GDPGTPase KRas / 0.732
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.732
3kkq GDPRas-related protein M-Ras / 0.731
4mkf AP5Adenylate kinase / 0.731
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.731
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.730
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.730
2fe4 GDPRas-related protein Rab-6B / 0.730
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.730
2bku GTPGTP-binding nuclear protein Ran / 0.729
2ce2 GDPGTPase HRas / 0.729
3oiu GNPGTPase HRas / 0.729
3zia ATPATP synthase subunit alpha, mitochondrial / 0.728
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.727
4asu ADPATP synthase subunit alpha, mitochondrial / 0.727
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.726
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.726
4jsy GTPMetallophosphoesterase / 0.726
4rkf GNPRas-related protein Rab-3 / 0.726
2zts ADPUncharacterized protein / 0.725
1x1r GDPRas-related protein M-Ras / 0.724
1zm7 TTPDeoxynucleoside kinase / 0.724
2fg5 GNPRas-related protein Rab-31 / 0.724
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.723
1mmg AGSMyosin-2 heavy chain / 0.723
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.723
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.723
3kz1 GSPTransforming protein RhoA / 0.721
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.720
2gcp GSPRho-related GTP-binding protein RhoC / 0.720
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.720
4dxa GSPRas-related protein Rap-1b / 0.719
4lhv GDPRas-related protein Rab-8A / 0.718
2l0x GDPGTP-binding protein Rheb / 0.717
3bbp GTPRas-related protein Rab-6A / 0.716
4luc GDPGTPase KRas / 0.716
3myk ANPMyosin-2 heavy chain / 0.715
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.714
3v4f GNPGTPase HRas / 0.714
5b2z GNPGTPase HRas / 0.714
2bme GNPRas-related protein Rab-4A / 0.713
2dpx GDPGTP-binding protein RAD / 0.713
2fna ADPUncharacterized protein / 0.713
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.712
4pjj ADPUnconventional myosin-VI / 0.712
3tnf GNPRas-related protein Rab-8A / 0.711
1cxz GSPTransforming protein RhoA / 0.710
1f5n GNPGuanylate-binding protein 1 / 0.710
1oix GDPRas-related protein Rab-11A / 0.710
2rgb GNPGTPase HRas / 0.710
4dvg GSPRho family GTPase / 0.710
4gp6 ADPMetallophosphoesterase / 0.710
1esn ANPPantothenate kinase 2.7.1.33 0.709
4dlw GNPGTPase HRas / 0.709
4lrw GDPGTPase KRas / 0.708
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.707
2osb AP5Adenylate kinase / 0.707
4epx GDPGTPase KRas / 0.706
4mit GTPRho-related protein racC / 0.706
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.705
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.702
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.702
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.702
4mkh AP5Adenylate kinase / 0.702
1eqy ATPActin, alpha skeletal muscle / 0.701
4lv6 GDPGTPase KRas / 0.700
3k3b ADPKinesin-like protein KIF11 / 0.699
4ihj GTPTubulin alpha-1B chain / 0.699
4pjk ADPMyosin-2 heavy chain / 0.699
2y65 ADPKinesin heavy chain / 0.698
4db1 ANPMyosin-7 / 0.698
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.696
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.695
2x2r ADPKinesin-like protein KIF11 / 0.695
1jx2 ADPMyosin-2 heavy chain / 0.694
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.694
4itr GDPCell division control protein 42 homolog / 0.693
1sdm ADPKinesin heavy chain-like protein / 0.692
1zio AP5Adenylate kinase / 0.692
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.692
4qbf AP5Adenylate kinase / 0.692
4tv9 GTPTubulin alpha-1B chain / 0.692
4ys0 ADPProtein translocase subunit SecA / 0.692
4tq9 GDPGTPase KRas / 0.691
1xts GTPGTP-binding protein Rheb / 0.689
4ldj GDPGTPase KRas / 0.689
4qos ADPPsp operon transcriptional activator / 0.689
2zet GTPRas-related protein Rab-27B / 0.688
3pcr GTPADP-ribosylation factor 6 / 0.688
1ake AP5Adenylate kinase / 0.687
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.687
4obe GDPGTPase KRas / 0.687
2xsz ATPRuvB-like 2 3.6.4.12 0.686
2gm1 ADPKinesin-like protein KIF11 / 0.685
4q02 GDPGTPase KRas / 0.685
5da9 AGSUncharacterized protein / 0.685
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
1sq5 ADPPantothenate kinase 2.7.1.33 0.683
1nsf ATPVesicle-fusing ATPase 3.6.4.6 0.682
2zr9 DTPProtein RecA / 0.682
3rep ATPIntegrin-linked protein kinase 2.7.11.1 0.682
2c96 ATPPsp operon transcriptional activator / 0.681
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.681
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.681
1dej ATPMajor actin / 0.680
1z0d GDPRas-related protein Rab-5C / 0.680
2eck ADPAdenylate kinase / 0.680
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.679
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.679
4nh0 ATPESX secretion system protein EccC / 0.679
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.677
2q36 ATPActin, alpha skeletal muscle / 0.677
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.677
1d5c GDPGTPase (Rab6) / 0.676
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.675
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.673
1sxj AGSReplication factor C subunit 1 / 0.672
3a6p GTPGTP-binding nuclear protein Ran / 0.672
3e5h GNPRas-related protein Rab-28 / 0.672
3kud GDPGTPase HRas / 0.672
4dsu GDPGTPase KRas / 0.672
4wbn GTPTubulin alpha-1B chain / 0.672
1xmv ADPProtein RecA / 0.670
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.670
2x3j ATPAcsD / 0.670
4a51 ADPKinesin-like protein KIF11 / 0.670
4hdq GNPRas-related protein Rap-1b / 0.670
4ohx ADPProtein clpf-1 / 0.670
1ss9 UPFLgtC / 0.669
1t44 ATPActin, alpha skeletal muscle / 0.669
3ea5 GDPGTP-binding nuclear protein Ran / 0.669
3g6x DGTDNA polymerase iota 2.7.7.7 0.669
4ol0 GTPGTP-binding nuclear protein Ran / 0.669
4qbh AP5Adenylate kinase / 0.669
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.667
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.667
4uj5 GNPRas-related protein Rab-11A / 0.667
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.666
3rmw UPGGlycogenin-1 2.4.1.186 0.666
4pkg ATPActin, alpha skeletal muscle / 0.666
1uad GNPRas-related protein Ral-A / 0.665
2b56 UTPRNA editing complex protein MP57 / 0.665
2eu8 AP5Adenylate kinase / 0.665
3nbx ADPATPase RavA 3.6.3 0.665
3tqc ADPPantothenate kinase / 0.665
4jl5 ADPAdenylate kinase / 0.665
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.664
3mn9 ATPActin-5C / 0.664
4o4i GTPTubulin alpha-1B chain / 0.664
2jcs TTPDeoxynucleoside kinase / 0.663
1fnn ADPORC1-type DNA replication protein / 0.662
4ww4 ADPRuvB-like helicase / 0.662
1svm ATPLarge T antigen 3.6.4 0.661
4cid ANPEH domain-containing protein 2 / 0.661
5dac AGSUncharacterized protein / 0.661
1bxr ANPCarbamoyl-phosphate synthase large chain / 0.660
2e8w IPEGeranylgeranyl pyrophosphate synthase / 0.660
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.660
4xj3 GTPCyclic GMP-AMP synthase / 0.660
5k5z ANPUncharacterized protein / 0.660
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
2x0q ATPAlcaligin biosynthesis protein / 0.659
4dto DCPDNA-directed DNA polymerase / 0.659
4qbg AP5Adenylate kinase / 0.659
1ibr GNPGTP-binding nuclear protein Ran / 0.658
1kmq GNPTransforming protein RhoA / 0.658
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
3bxz ADPProtein translocase subunit SecA / 0.658
4dsn GCPGTPase KRas / 0.658
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.657
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.657
2vf7 ADPUvrABC system protein A / 0.657
3mn6 ATPActin-5C / 0.656
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.656
4dxj 0M9Farnesyl pyrophosphate synthase / 0.656
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.656
1w5t ANPORC1-type DNA replication protein 2 / 0.655
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.655
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
2w02 ATPAcsD / 0.655
4u03 GTPCyclic GMP-AMP synthase / 0.655
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.654
1k5d GNPGTP-binding nuclear protein Ran / 0.654
2d7d ADPUvrABC system protein B / 0.654
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.654
5bsm ATP4-coumarate--CoA ligase 2 6.2.1.12 0.654
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.653
1qz5 ATPActin, alpha skeletal muscle / 0.653
4k41 ATPActin, alpha skeletal muscle / 0.653
4qfy DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.653
1yhn GTPRas-related protein Rab-7a / 0.652
3au2 DGTDNA polymerase beta family (X family) / 0.652
3ryh GTPTubulin alpha chain / 0.652
3vhx GTPADP-ribosylation factor 6 / 0.652
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.651
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.650
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.650
2v51 ATPActin, alpha skeletal muscle / 0.650
4cf7 ADPAdenylate kinase / 0.650
4iij GTPTubulin alpha-1B chain / 0.650