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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
3ryh GTP Tubulin alpha chain

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3ryh GTPTubulin alpha chain / 1.362
4ihj GTPTubulin alpha-1B chain / 1.242
5jqg GTPTubulin alpha-1B chain / 1.238
4tv9 GTPTubulin alpha-1B chain / 1.234
4wbn GTPTubulin alpha-1B chain / 1.215
5la6 GTPTubulin alpha-1B chain / 1.202
5itz GTPTubulin alpha-1B chain / 1.183
4tuy GTPTubulin alpha-1B chain / 1.169
4o4l GTPTubulin alpha-1B chain / 1.168
4zol GTPTubulin alpha-1B chain / 1.155
4iij GTPTubulin alpha-1B chain / 1.123
4yj2 GTPTubulin alpha-1B chain / 1.059
4o4i GTPTubulin alpha-1B chain / 1.030
3cb2 GDPTubulin gamma-1 chain / 0.953
4f6r GDPTubulin beta chain / 0.862
3zid GDPTubulin-like protein CetZ / 0.853
4b45 GSPTubulin-like protein CetZ2 / 0.813
4ffb GTPTubulin alpha-1 chain / 0.789
5la6 GDPTubulin beta-2B chain / 0.777
2xka GSPCell division protein FtsZ / 0.743
4u3j GTPTubulin beta chain / 0.742
1w5a GTPCell division protein FtsZ 1 / 0.731
3m0e ATPTranscriptional regulator (NtrC family) / 0.709
1w5b GTPCell division protein FtsZ 1 / 0.708
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.706
1z5w GTPTubulin gamma-1 chain / 0.695
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.686
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.686
1wua ATPActin, alpha skeletal muscle / 0.685
5ahk TPPAcetolactate synthase II, large subunit / 0.685
4qm6 GTPMetallophosphoesterase / 0.684
4tyq AP5Adenylate kinase / 0.683
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.681
3s8a DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.680
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.678
1xje TTPVitamin B12-dependent ribonucleotide reductase / 0.677
4dwb 0M7Farnesyl pyrophosphate synthase / 0.677
4fl2 ANPTyrosine-protein kinase SYK 2.7.10.2 0.677
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.675
3wt0 ATPCell division protein FtsA / 0.674
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.673
4pki ATPActin, alpha skeletal muscle / 0.672
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.671
3vhx GTPADP-ribosylation factor 6 / 0.671
4fvq ATPTyrosine-protein kinase JAK2 / 0.671
4pkg ATPActin, alpha skeletal muscle / 0.671
3a5o ATPMajor actin / 0.670
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.669
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.668
1s22 ATPActin, alpha skeletal muscle / 0.668
1t44 ATPActin, alpha skeletal muscle / 0.668
2gcp GSPRho-related GTP-binding protein RhoC / 0.668
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.668
3o0o TTPVitamin B12-dependent ribonucleotide reductase / 0.668
4k41 ATPActin, alpha skeletal muscle / 0.668
1dej ATPMajor actin / 0.667
1pox TPPPyruvate oxidase 1.2.3.3 0.667
1qz5 ATPActin, alpha skeletal muscle / 0.667
2e8w IPEGeranylgeranyl pyrophosphate synthase / 0.667
2q36 ATPActin, alpha skeletal muscle / 0.667
4nu0 AP5Adenylate kinase / 0.667
4w5j AP5Adenylate kinase / 0.667
1fmw ATPMyosin-2 heavy chain / 0.666
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.666
5i4n ATPTyrosine-protein kinase JAK2 / 0.666
1c0f ATPMajor actin / 0.665
2a41 ATPActin, alpha skeletal muscle / 0.665
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.665
2q16 ITTdITP/XTP pyrophosphatase / 0.665
4b1v ATPActin, alpha skeletal muscle / 0.665
1kxp ATPActin, alpha skeletal muscle / 0.664
2c42 TPPPyruvate synthase / 0.664
4mkg AP5Adenylate kinase / 0.664
2qaj AP5Adenylate kinase / 0.663
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.662
1z5v GSPTubulin gamma-1 chain / 0.662
2o1o RISPutative farnesyl pyrophosphate synthase / 0.662
3vth APCCarbamoyltransferase / 0.662
2osb AP5Adenylate kinase / 0.661
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.661
4xvu ATPATPase GET3 / 0.661
2ywv ADPPhosphoribosylaminoimidazole-succinocarboxamide synthase / 0.660
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.659
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.659
1cxz GSPTransforming protein RhoA / 0.658
1peq TTPRibonucleoside-diphosphate reductase 2 subunit alpha 1.17.4.1 0.658
3m6g ATPActin, alpha skeletal muscle / 0.658
3qbt GNPRas-related protein Rab-8A / 0.658
4db1 ANPMyosin-7 / 0.658
1mez GDPAdenylosuccinate synthetase isozyme 1 / 0.657
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.656
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.656
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.656
1gwn GTPRho-related GTP-binding protein RhoE / 0.655
1mb9 ATPCarboxyethyl-arginine beta-lactam-synthase 6.3.3.4 0.654
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.654
2oan ATPActin, cytoplasmic 1 / 0.654
2rgx AP5Adenylate kinase / 0.654
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.654
3mhy ATPNitrogen regulatory protein P-II 1 / 0.654
3wqu ATPCell division protein FtsA / 0.654
2npi ATPmRNA cleavage and polyadenylation factor CLP1 / 0.653
2q97 ATPActin, alpha skeletal muscle / 0.653
3eku ATPActin-5C / 0.653
4ol0 GTPGTP-binding nuclear protein Ran / 0.653
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.652
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.652
2eu8 AP5Adenylate kinase / 0.651
3daw ATPActin, alpha skeletal muscle / 0.651
3gfz C2EUncharacterized protein / 0.651
3mn9 ATPActin-5C / 0.651
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
2rgg GNPGTPase HRas / 0.650
3nbz GTPGTP-binding nuclear protein Ran / 0.650
4pl8 ATPActin, alpha skeletal muscle / 0.650