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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
3hpr AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3hpr AP5Adenylate kinase / 1.739
3hpq AP5Adenylate kinase / 1.374
4x8l AP5Adenylate kinase / 1.309
1e4v AP5Adenylate kinase / 1.197
1ake AP5Adenylate kinase / 0.999
4x8o AP5Adenylate kinase / 0.991
4qbh AP5Adenylate kinase / 0.927
1e4y AP5Adenylate kinase / 0.905
2eck ADPAdenylate kinase / 0.872
2rgx AP5Adenylate kinase / 0.851
4qbi AP5Adenylate kinase / 0.849
1ank ANPAdenylate kinase / 0.816
4jl5 ADPAdenylate kinase / 0.813
4jl6 ADPAdenylate kinase / 0.809
1zio AP5Adenylate kinase / 0.795
4jky ADPAdenylate kinase / 0.788
4qbg AP5Adenylate kinase / 0.786
4mkh AP5Adenylate kinase / 0.780
4dxa GSPRas-related protein Rap-1b / 0.777
4jlb ADPAdenylate kinase / 0.776
4dlt GNPGTPase HRas / 0.775
4o25 GTPGTP-binding protein Rheb / 0.773
4qbf AP5Adenylate kinase / 0.763
5c46 GSPRas-related protein Rab-11A / 0.762
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.761
3aky AP5Adenylate kinase / 0.756
3lbn GNPGTPase HRas / 0.754
5b2z GNPGTPase HRas / 0.746
5k5z ANPUncharacterized protein / 0.746
2aky AP5Adenylate kinase / 0.745
3l8y GNPGTPase HRas / 0.745
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.743
2vf7 ADPUvrABC system protein A / 0.742
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.740
1w5s ADPORC1-type DNA replication protein 2 / 0.739
1z6t ADPApoptotic protease-activating factor 1 / 0.739
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.736
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.736
2uyi ADPKinesin-like protein KIF11 / 0.734
5aun ADPIron-sulfur cluster carrier protein / 0.732
2ql6 ADPNicotinamide riboside kinase 1 / 0.731
3rs4 GNPGTPase HRas / 0.730
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.729
3rs0 GNPGTPase HRas / 0.729
3oiv GNPGTPase HRas / 0.728
3rsl GNPGTPase HRas / 0.728
4uj3 GNPRas-related protein Rab-11A / 0.727
3oiw GNPGTPase HRas / 0.726
1p3j AP5Adenylate kinase / 0.725
2x2r ADPKinesin-like protein KIF11 / 0.725
4nh0 ATPESX secretion system protein EccC / 0.722
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.720
4kvg GTPRas-related protein Rap-1A / 0.720
4mkg AP5Adenylate kinase / 0.720
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.719
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.719
2x7e ADPKinesin-like protein KIF11 / 0.718
4q03 GDPGTPase KRas / 0.718
4y0v GDPADP-ribosylation factor 1, putative / 0.718
4ylg GDPADP-ribosylation factor 1, putative / 0.718
1z0d GDPRas-related protein Rab-5C / 0.717
3tso GNPRas-related protein Rab-25 / 0.717
4asu ADPATP synthase subunit alpha, mitochondrial / 0.717
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.716
1fmw ATPMyosin-2 heavy chain / 0.715
4dlv GNPGTPase HRas / 0.715
4b7b ADPKinesin-like protein KIF11 / 0.714
3k8y GNPGTPase HRas / 0.713
1kmq GNPTransforming protein RhoA / 0.712
1s3g AP5Adenylate kinase / 0.712
1l8q ADPChromosomal replication initiator protein DnaA / 0.711
3dkv AP5Adenylate kinase / 0.711
4l9s GDPGTPase HRas / 0.709
2fna ADPUncharacterized protein / 0.708
3c41 ANPAmino acid ABC transporter / 0.708
4d81 ADPAAA ATPase, central domain protein / 0.706
4jl8 ADPAdenylate kinase / 0.706
5fl3 ADPPili retraction protein PilT / 0.706
4lpk GDPGTPase KRas / 0.705
2fe4 GDPRas-related protein Rab-6B / 0.704
3lbi GNPGTPase HRas / 0.704
2gm1 ADPKinesin-like protein KIF11 / 0.703
2rgb GNPGTPase HRas / 0.702
2rgc GNPGTPase HRas / 0.702
4dlw GNPGTPase HRas / 0.702
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.702
3tlx ADPAdenylate kinase 2 / 0.701
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.700
3kkq GDPRas-related protein M-Ras / 0.700
3k3b ADPKinesin-like protein KIF11 / 0.699
3rs7 GNPGTPase HRas / 0.699
1sdm ADPKinesin heavy chain-like protein / 0.698
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.698
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.698
2bme GNPRas-related protein Rab-4A / 0.696
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.696
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.696
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.694
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.694
3ref GDPRho family GTPase / 0.694
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.691
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.690
2c9o ADPRuvB-like 1 3.6.4.12 0.690
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.689
1yrs ADPKinesin-like protein KIF11 / 0.689
2oo7 AP5Adenylate kinase / 0.689
1w5t ANPORC1-type DNA replication protein 2 / 0.688
2q2z ADPKinesin-like protein KIF11 / 0.688
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.686
4nu0 AP5Adenylate kinase / 0.686
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.685
1b7t ADPMyosin heavy chain, striated muscle / 0.685
4dls GNPGTPase HRas / 0.685
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.685
5l3s GNPSignal recognition particle receptor FtsY / 0.683
3uk6 ADPRuvB-like 2 3.6.4.12 0.682
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
3rs5 GNPGTPase HRas / 0.681
3tqc ADPPantothenate kinase / 0.680
4jlp ADPAdenylate kinase / 0.680
4xvr GNPGTPase HRas / 0.680
1mab ATPATP synthase subunit alpha, mitochondrial / 0.679
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.679
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
4jld ADPAdenylate kinase / 0.678
4qos ADPPsp operon transcriptional activator / 0.678
1sq5 ADPPantothenate kinase 2.7.1.33 0.676
4jlo ADPAdenylate kinase / 0.676
4typ AP5Adenylate kinase / 0.676
4w5j AP5Adenylate kinase / 0.676
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.675
4cf7 ADPAdenylate kinase / 0.675
4ike ADPAdenylate kinase / 0.674
3i3s GNPGTPase HRas / 0.673
1hwl ADP3-hydroxy-3-methylglutaryl-coenzyme A reductase 1.1.1.34 0.672
3tnf GNPRas-related protein Rab-8A / 0.672
4ww4 ADPRuvB-like helicase / 0.672
5c1o ANPD-alanine--D-alanine ligase / 0.670
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.669
1p9w ANPType II secretion system protein E / 0.668
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.668
1ii6 ADPKinesin-like protein KIF11 / 0.662
1mma ADPMyosin-2 heavy chain / 0.662
1v8k ANPKinesin-like protein KIF2C / 0.662
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.662
4epx GDPGTPase KRas / 0.662
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.661
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.660
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.660
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.660
2fsn ADPArchaeal actin homolog / 0.659
4d0l GSPRas-related protein Rab-11A / 0.659
2eh2 SAHDiphthine synthase / 0.658
3v4f GNPGTPase HRas / 0.658
4ehy ADPTetraacyldisaccharide 4'-kinase / 0.658
2ha8 SAHProbable methyltransferase TARBP1 / 0.656
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.655
1esn ANPPantothenate kinase 2.7.1.33 0.654
3ffk ATPActin, alpha skeletal muscle / 0.654
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.653
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.652
4mkf AP5Adenylate kinase / 0.652
3a8t ATPAdenylate isopentenyltransferase / 0.651
1cgp CMPcAMP-activated global transcriptional regulator CRP / 0.650
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.650
1oe0 TTPDeoxynucleoside kinase / 0.650
3d8b ADPFidgetin-like protein 1 3.6.4 0.650