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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
4yj2 GTP Tubulin alpha-1B chain

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4yj2 GTPTubulin alpha-1B chain / 1.329
4tv9 GTPTubulin alpha-1B chain / 1.188
4wbn GTPTubulin alpha-1B chain / 1.186
5jqg GTPTubulin alpha-1B chain / 1.184
4ihj GTPTubulin alpha-1B chain / 1.182
4zol GTPTubulin alpha-1B chain / 1.181
5la6 GTPTubulin alpha-1B chain / 1.169
4tuy GTPTubulin alpha-1B chain / 1.159
5itz GTPTubulin alpha-1B chain / 1.131
4o4l GTPTubulin alpha-1B chain / 1.127
4iij GTPTubulin alpha-1B chain / 1.115
4o4i GTPTubulin alpha-1B chain / 1.075
3ryh GTPTubulin alpha chain / 1.059
3zid GDPTubulin-like protein CetZ / 0.863
4ffb GTPTubulin alpha-1 chain / 0.845
3cb2 GDPTubulin gamma-1 chain / 0.809
5la6 GDPTubulin beta-2B chain / 0.782
4f6r GDPTubulin beta chain / 0.743
4u3j GTPTubulin beta chain / 0.734
1z5v GSPTubulin gamma-1 chain / 0.726
2xka GSPCell division protein FtsZ / 0.724
1w5a GTPCell division protein FtsZ 1 / 0.719
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.714
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.712
4fvq ATPTyrosine-protein kinase JAK2 / 0.711
5ahk TPPAcetolactate synthase II, large subunit / 0.701
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.700
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.698
1xje TTPVitamin B12-dependent ribonucleotide reductase / 0.696
3m0e ATPTranscriptional regulator (NtrC family) / 0.694
3vth APCCarbamoyltransferase / 0.693
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.693
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.691
2a41 ATPActin, alpha skeletal muscle / 0.687
4pki ATPActin, alpha skeletal muscle / 0.685
2aky AP5Adenylate kinase / 0.684
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.683
2qaj AP5Adenylate kinase / 0.682
4dwb 0M7Farnesyl pyrophosphate synthase / 0.682
3ahj TPPProbable phosphoketolase / 0.681
4mkf AP5Adenylate kinase / 0.677
1pox TPPPyruvate oxidase 1.2.3.3 0.676
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.676
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.675
4qm6 GTPMetallophosphoesterase / 0.675
2xul ATPNitrogen regulatory protein P-II / 0.674
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.673
3ffk ATPActin, alpha skeletal muscle / 0.673
1yxq ATPActin, alpha skeletal muscle / 0.672
1fmw ATPMyosin-2 heavy chain / 0.671
1s22 ATPActin, alpha skeletal muscle / 0.671
1w5b GTPCell division protein FtsZ 1 / 0.671
1peq TTPRibonucleoside-diphosphate reductase 2 subunit alpha 1.17.4.1 0.670
1wua ATPActin, alpha skeletal muscle / 0.670
3wt0 ATPCell division protein FtsA / 0.669
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.668
3s8a DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.668
1z5w GTPTubulin gamma-1 chain / 0.667
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.667
1qz5 ATPActin, alpha skeletal muscle / 0.666
3m1f ATPActin, alpha skeletal muscle / 0.666
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.665
4bzb DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.665
5i4n ATPTyrosine-protein kinase JAK2 / 0.664
2ywv ADPPhosphoribosylaminoimidazole-succinocarboxamide synthase / 0.663
4ol0 GTPGTP-binding nuclear protein Ran / 0.663
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.662
3krf DSTGeranyl diphosphate synthase large subunit / 0.661
1dej ATPMajor actin / 0.660
3el2 ATPActin-5C / 0.660
4k41 ATPActin, alpha skeletal muscle / 0.660
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.659
1jsz NDMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 2.1.1.57 0.658
2v9x DUTdCTP deaminase / 0.658
3m6g ATPActin, alpha skeletal muscle / 0.658
3w3d ATPActin, gamma-enteric smooth muscle / 0.658
3ahi HTLProbable phosphoketolase / 0.657
4ehu ANP2-hydroxyisocaproyl-CoA dehydratase activator / 0.656
4fyx UTPAspartate carbamoyltransferase regulatory chain / 0.655
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.655
5c4i TPPOxalate oxidoreductase subunit alpha / 0.655
5c4i TPPOxalate oxidoreductase subunit beta / 0.655
1t44 ATPActin, alpha skeletal muscle / 0.654
3a5o ATPMajor actin / 0.654
3dyl PCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A / 0.654
3mn9 ATPActin-5C / 0.654
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.654
1p3j AP5Adenylate kinase / 0.653
4xj3 GTPCyclic GMP-AMP synthase / 0.653
1lot ATPActin, alpha skeletal muscle / 0.651
2npi ATPmRNA cleavage and polyadenylation factor CLP1 / 0.651
3wqu ATPCell division protein FtsA / 0.651
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
3mhy ATPNitrogen regulatory protein P-II 1 / 0.650
3myk ANPMyosin-2 heavy chain / 0.650
4cbx ATPActin-2 / 0.650