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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
4x8l AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4x8l AP5Adenylate kinase / 1.881
4x8o AP5Adenylate kinase / 1.574
3hpq AP5Adenylate kinase / 1.314
3hpr AP5Adenylate kinase / 1.309
1e4v AP5Adenylate kinase / 1.144
2rgx AP5Adenylate kinase / 1.059
4jl8 ADPAdenylate kinase / 0.990
1p3j AP5Adenylate kinase / 0.926
2osb AP5Adenylate kinase / 0.912
4qbh AP5Adenylate kinase / 0.892
4jlb ADPAdenylate kinase / 0.886
4mkf AP5Adenylate kinase / 0.885
4qbf AP5Adenylate kinase / 0.880
2eck ADPAdenylate kinase / 0.879
3aky AP5Adenylate kinase / 0.871
2oo7 AP5Adenylate kinase / 0.869
4qbg AP5Adenylate kinase / 0.869
4qbi AP5Adenylate kinase / 0.852
4jl6 ADPAdenylate kinase / 0.851
4jl5 ADPAdenylate kinase / 0.848
4ike ADPAdenylate kinase / 0.842
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.841
4jld ADPAdenylate kinase / 0.841
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.840
2aky AP5Adenylate kinase / 0.831
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.830
4tyq AP5Adenylate kinase / 0.827
2c9o ADPRuvB-like 1 3.6.4.12 0.823
4jla ADPAdenylate kinase / 0.817
4mkh AP5Adenylate kinase / 0.817
1e4y AP5Adenylate kinase / 0.816
4jlo ADPAdenylate kinase / 0.816
1ank ANPAdenylate kinase / 0.805
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.803
4jky ADPAdenylate kinase / 0.789
4mkg AP5Adenylate kinase / 0.785
2r9v ATPATP synthase subunit alpha / 0.784
1w5t ANPORC1-type DNA replication protein 2 / 0.782
3tlx ADPAdenylate kinase 2 / 0.778
3dkv AP5Adenylate kinase / 0.776
1d5c GDPGTPase (Rab6) / 0.775
2eu8 AP5Adenylate kinase / 0.772
4jlp ADPAdenylate kinase / 0.770
4l9s GDPGTPase HRas / 0.766
1s3g AP5Adenylate kinase / 0.762
4ql3 GDPGTPase KRas / 0.762
2ffq GSPRas-related protein Rab-6B / 0.756
1kmq GNPTransforming protein RhoA / 0.753
2qaj AP5Adenylate kinase / 0.750
1okk GCPSignal recognition particle protein / 0.749
1okk GCPSignal recognition particle receptor FtsY / 0.749
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.749
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.749
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.746
3tnf GNPRas-related protein Rab-8A / 0.746
3r9x GNPGTPase Era / 0.745
4i1v ADPDephospho-CoA kinase / 0.745
5aun ADPIron-sulfur cluster carrier protein / 0.745
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.743
1yzq GNPRas-related protein Rab-6A / 0.741
2vf7 ADPUvrABC system protein A / 0.741
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.739
1z2c GNPRho-related GTP-binding protein RhoC / 0.738
4dxa GSPRas-related protein Rap-1b / 0.736
4o2l GTPGTP-binding protein Rheb / 0.736
5cyo GDPSeptin-9 / 0.733
1sq5 ADPPantothenate kinase 2.7.1.33 0.732
3b1x GNPFerrous iron transport protein B / 0.730
4uj5 GNPRas-related protein Rab-11A / 0.729
2j7p GNPSignal recognition particle protein / 0.728
2j7p GNPSignal recognition particle receptor FtsY / 0.728
3dl0 AP5Adenylate kinase / 0.728
2ql6 ADPNicotinamide riboside kinase 1 / 0.726
2fe4 GDPRas-related protein Rab-6B / 0.725
1ake AP5Adenylate kinase / 0.723
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.722
4yqf GDPSeptin-9 / 0.721
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.720
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.720
1yu9 GNPRas-related protein Rab-4A / 0.720
2gcp GSPRho-related GTP-binding protein RhoC / 0.718
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.718
3kkq GDPRas-related protein M-Ras / 0.718
3uk6 ADPRuvB-like 2 3.6.4.12 0.718
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.717
1ny5 ADPTranscriptional regulator (NtrC family) / 0.716
2q3f GNPRas-related GTP-binding protein D / 0.716
4epx GDPGTPase KRas / 0.716
1fnn ADPORC1-type DNA replication protein / 0.715
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.715
4nu0 AP5Adenylate kinase / 0.715
4g0n GNPGTPase HRas / 0.713
3ref GDPRho family GTPase / 0.710
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.709
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.709
3oiw GNPGTPase HRas / 0.709
4gp6 ADPMetallophosphoesterase / 0.709
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.708
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.707
3c15 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.706
1zio AP5Adenylate kinase / 0.705
2bku GTPGTP-binding nuclear protein Ran / 0.704
2xae ADPKinesin-like protein KIF11 / 0.701
4qnr ATPPsp operon transcriptional activator / 0.700
3zia ATPATP synthase subunit alpha, mitochondrial / 0.699
4q03 GDPGTPase KRas / 0.699
1p9w ANPType II secretion system protein E / 0.695
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.695
3oiu GNPGTPase HRas / 0.695
1f5n GNPGuanylate-binding protein 1 / 0.692
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.692
3oiv GNPGTPase HRas / 0.691
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.691
3kuc GDPRas-related protein Rap-1A / 0.689
2hld ANPATP synthase subunit alpha, mitochondrial / 0.688
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.688
4l9w GNPGTPase HRas / 0.688
1vg8 GNPRas-related protein Rab-7a / 0.685
4typ AP5Adenylate kinase / 0.685
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.684
2bbw GP5Adenylate kinase 4, mitochondrial / 0.682
2rgg GNPGTPase HRas / 0.681
3eg5 GNPCell division control protein 42 homolog / 0.680
4w5j AP5Adenylate kinase / 0.680
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.678
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.678
4o2r GDPGTP-binding protein Rheb / 0.678
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.677
4jsy GTPMetallophosphoesterase / 0.676
1yrs ADPKinesin-like protein KIF11 / 0.675
4cid ANPEH domain-containing protein 2 / 0.674
1a4r GNHCell division control protein 42 homolog / 0.671
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.671
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
1esn ANPPantothenate kinase 2.7.1.33 0.671
1w5t ADPORC1-type DNA replication protein 2 / 0.670
1fmw ATPMyosin-2 heavy chain / 0.669
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.668
3q9l ATPSeptum site-determining protein MinD / 0.668
5d3q GDPDynamin-1 3.6.5.5 0.668
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.667
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.666
2l0x GDPGTP-binding protein Rheb / 0.666
4xvu ATPATPase GET3 / 0.666
1ii6 ADPKinesin-like protein KIF11 / 0.663
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.663
1rfu ADPPyridoxal kinase 2.7.1.35 0.662
4nyi GNPGTPase HRas / 0.662
1xtr GNPGTP-binding protein Rheb / 0.661
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.660
3tw6 ADPPyruvate carboxylase / 0.660
4ffl ADPUncharacterized protein / 0.660
2rgb GNPGTPase HRas / 0.659
4ohx ADPProtein clpf-1 / 0.659
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.658
2rgc GNPGTPase HRas / 0.658
3rs4 GNPGTPase HRas / 0.658
5jlj GNPGTP-binding nuclear protein Ran / 0.657
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.656
4a1z ADPKinesin-like protein KIF11 / 0.655
4dlz GNPGTPase HRas / 0.655
4qm6 GTPMetallophosphoesterase / 0.655
1l8q ADPChromosomal replication initiator protein DnaA / 0.654
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.654
4fu0 ADPD-alanine--D-alanine ligase / 0.654
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.653
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.653
3zfd ANPChromosome-associated kinesin KIF4 / 0.653
4ys0 ADPProtein translocase subunit SecA / 0.653
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.652
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.652
4g01 GDPRas-related protein RABF2b / 0.651
3d8b ADPFidgetin-like protein 1 3.6.4 0.650