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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
4qbg AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4qbg AP5Adenylate kinase / 1.653
4mkg AP5Adenylate kinase / 1.133
4mkh AP5Adenylate kinase / 1.127
2eu8 AP5Adenylate kinase / 1.098
3dl0 AP5Adenylate kinase / 1.074
4mkf AP5Adenylate kinase / 1.069
2oo7 AP5Adenylate kinase / 1.039
4tyq AP5Adenylate kinase / 1.030
3dkv AP5Adenylate kinase / 1.017
2rgx AP5Adenylate kinase / 0.950
4nu0 AP5Adenylate kinase / 0.950
1zio AP5Adenylate kinase / 0.938
4w5j AP5Adenylate kinase / 0.932
4jl8 ADPAdenylate kinase / 0.922
4qbf AP5Adenylate kinase / 0.903
4x8l AP5Adenylate kinase / 0.869
1e4v AP5Adenylate kinase / 0.854
4qbh AP5Adenylate kinase / 0.836
4jsy GTPMetallophosphoesterase / 0.827
1p3j AP5Adenylate kinase / 0.826
4qbi AP5Adenylate kinase / 0.823
4jl5 ADPAdenylate kinase / 0.812
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.807
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.807
4jla ADPAdenylate kinase / 0.803
2ql6 ADPNicotinamide riboside kinase 1 / 0.799
4jlo ADPAdenylate kinase / 0.799
4jlb ADPAdenylate kinase / 0.797
2eck ADPAdenylate kinase / 0.796
4jld ADPAdenylate kinase / 0.796
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.794
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.792
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.791
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.791
1w5s ADPORC1-type DNA replication protein 2 / 0.790
2qaj AP5Adenylate kinase / 0.790
4jl6 ADPAdenylate kinase / 0.790
3hpr AP5Adenylate kinase / 0.786
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.782
2osb AP5Adenylate kinase / 0.781
3hpq AP5Adenylate kinase / 0.780
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.777
4qnr ATPPsp operon transcriptional activator / 0.773
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.771
3zia ATPATP synthase subunit alpha, mitochondrial / 0.770
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.767
4qos ADPPsp operon transcriptional activator / 0.766
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.765
4jky ADPAdenylate kinase / 0.762
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.752
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.751
4ike ADPAdenylate kinase / 0.751
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.750
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.750
5cyo GDPSeptin-9 / 0.750
3t1t GDPProbable gliding protein mglA / 0.746
4mit GTPRho-related protein racC / 0.745
1ank ANPAdenylate kinase / 0.739
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.739
3r9i ADPSeptum site-determining protein MinD / 0.733
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.731
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.729
2aky AP5Adenylate kinase / 0.729
4idn GNPAtlastin-1 3.6.5 0.729
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.727
3myk ANPMyosin-2 heavy chain / 0.723
3l9h ADPKinesin-like protein KIF11 / 0.720
2bbw GP5Adenylate kinase 4, mitochondrial / 0.719
2c9c ATPPsp operon transcriptional activator / 0.718
2c9o ADPRuvB-like 1 3.6.4.12 0.717
2hld ANPATP synthase subunit alpha, mitochondrial / 0.716
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.716
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.716
3c41 ANPAmino acid ABC transporter / 0.714
2vf7 ADPUvrABC system protein A / 0.713
2xsz ATPRuvB-like 2 3.6.4.12 0.713
5d3q GDPDynamin-1 3.6.5.5 0.713
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.712
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.712
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.710
3l1c ADPProtein claret segregational / 0.710
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.708
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.703
1p9w ANPType II secretion system protein E / 0.702
4ww4 ADPRuvB-like helicase / 0.702
1ii6 ADPKinesin-like protein KIF11 / 0.696
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.694
2r9v ATPATP synthase subunit alpha / 0.694
5fl3 ADPPili retraction protein PilT / 0.692
4hse ADPChaperone protein ClpB / 0.690
3fkq ATPNtrC-like two-domain protein / 0.689
4nyi GNPGTPase HRas / 0.687
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.686
1wdt GTPElongation factor G (EF-G-2) / 0.684
3k1j ADPATP-dependent protease Lon / 0.683
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.681
1fmw ATPMyosin-2 heavy chain / 0.678
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.678
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.675
2fl2 ADPKinesin-like protein KIF11 / 0.674
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.674
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.673
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.673
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.673
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.673
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.673
3pcr GTPADP-ribosylation factor 6 / 0.672
4c30 ANPDNA helicase / 0.672
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.672
1svw GTPProbable GTP-binding protein EngB / 0.671
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.670
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.670
4nyj GNPGTPase HRas / 0.669
1e4y AP5Adenylate kinase / 0.668
1e32 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.665
1a2b GSPTransforming protein RhoA / 0.663
4js0 GNPCell division control protein 42 homolog / 0.663
1m7b GTPRho-related GTP-binding protein RhoE / 0.662
2ffq GSPRas-related protein Rab-6B / 0.662
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.661
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.660
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.659
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.659
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.659
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.658
3aky AP5Adenylate kinase / 0.657
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.657
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.656
2a5y ATPCell death protein 4 / 0.656
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.656
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.656
3mjh GTPRas-related protein Rab-5A / 0.655
1oe0 TTPDeoxynucleoside kinase / 0.654
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.653
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.653
3qbv GDPCell division control protein 42 homolog / 0.653
5da9 AGSUncharacterized protein / 0.653
5iqi GNPBifunctional AAC/APH 2.3.1 0.652
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.652
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.651
4gvz ADPArginine kinase 2.7.3.3 0.651
1nhh ANPDNA mismatch repair protein MutL / 0.650
2c96 ATPPsp operon transcriptional activator / 0.650
4dlv GNPGTPase HRas / 0.650
4h5d YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.650