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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
4pkg ATP Actin, alpha skeletal muscle

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4pkg ATPActin, alpha skeletal muscle / 1.181
1qz5 ATPActin, alpha skeletal muscle / 1.160
1s22 ATPActin, alpha skeletal muscle / 1.160
4k41 ATPActin, alpha skeletal muscle / 1.159
1wua ATPActin, alpha skeletal muscle / 1.146
4b1v ATPActin, alpha skeletal muscle / 1.131
4pki ATPActin, alpha skeletal muscle / 1.124
1c0f ATPMajor actin / 1.118
1t44 ATPActin, alpha skeletal muscle / 1.110
1dej ATPMajor actin / 1.105
3a5o ATPMajor actin / 1.098
3m6g ATPActin, alpha skeletal muscle / 1.097
4pl8 ATPActin, alpha skeletal muscle / 1.089
3w3d ATPActin, gamma-enteric smooth muscle / 1.081
2q36 ATPActin, alpha skeletal muscle / 1.071
1eqy ATPActin, alpha skeletal muscle / 1.070
3mn9 ATPActin-5C / 1.066
2v51 ATPActin, alpha skeletal muscle / 1.053
2q97 ATPActin, alpha skeletal muscle / 1.046
5ce3 ATPActin / 1.045
3chw ATPMajor actin / 1.036
3m1f ATPActin, alpha skeletal muscle / 1.032
3eku ATPActin-5C / 1.031
3mn6 ATPActin-5C / 1.026
3tu5 ATPActin, alpha skeletal muscle / 1.021
3daw ATPActin, alpha skeletal muscle / 1.020
1kxp ATPActin, alpha skeletal muscle / 1.017
3eks ATPActin-5C / 1.014
1mdu ATPActin, alpha skeletal muscle / 0.997
3mn7 ATPActin-5C / 0.996
1rgi ATPActin, alpha skeletal muscle / 0.987
4cbx ATPActin-2 / 0.986
1nlv ATPMajor actin / 0.982
3ffk ATPActin, alpha skeletal muscle / 0.971
2a41 ATPActin, alpha skeletal muscle / 0.963
3el2 ATPActin-5C / 0.928
4pkh ADPActin, alpha skeletal muscle / 0.920
2p9k ATPActin-related protein 2 / 0.918
2oan ATPActin, cytoplasmic 1 / 0.910
4m63 ATPActin-5C / 0.883
1atn ATPActin, alpha skeletal muscle / 0.877
1h1v ATPActin, alpha skeletal muscle / 0.877
4ci6 ATPActin / 0.877
1lot ATPActin, alpha skeletal muscle / 0.869
4b9q ATPChaperone protein DnaK / 0.867
3wt0 ATPCell division protein FtsA / 0.850
4k42 ADPActin, alpha skeletal muscle / 0.842
3a5m ATPMajor actin / 0.832
3d2e ATPHeat shock protein homolog SSE1 / 0.817
4ehu ANP2-hydroxyisocaproyl-CoA dehydratase activator / 0.810
1ijj ATPActin, alpha skeletal muscle / 0.806
1rfq ATPActin, alpha skeletal muscle / 0.794
4eht ADP2-hydroxyisocaproyl-CoA dehydratase activator / 0.794
1yxq ATPActin, alpha skeletal muscle / 0.787
1nm1 ATPMajor actin / 0.774
3ule ATPActin-related protein 2 / 0.744
1nmd ATPMajor actin / 0.743
4a62 ANPPlasmid segregation protein ParM / 0.738
2e2q ADPATP-dependent hexokinase / 0.736
3wqt ANPCell division protein FtsA / 0.736
4brg GNPEctonucleoside triphosphate diphosphohydrolase I / 0.733
4a61 ANPPlasmid segregation protein ParM / 0.725
2d0o ADPDiol dehydratase-reactivating factor alpha subunit / 0.724
3u4l ATPActin, cytoplasmic 1 / 0.722
4k43 ADPActin, alpha skeletal muscle / 0.721
2fsn ADPArchaeal actin homolog / 0.718
3ldo ANP78 kDa glucose-regulated protein / 0.713
5bsm ATP4-coumarate--CoA ligase 2 6.2.1.12 0.702
4brd ANPEctonucleoside triphosphate diphosphohydrolase I / 0.701
2zgz GNPPlasmid segregation protein ParM / 0.698
4jhd ANPActin-5C / 0.695
1mwm ADPPlasmid segregation protein ParM / 0.694
5f1x ATP78 kDa glucose-regulated protein / 0.692
1ngd ADPHeat shock cognate 71 kDa protein / 0.690
2zgy GDPPlasmid segregation protein ParM / 0.690
4bri UNPEctonucleoside triphosphate diphosphohydrolase I / 0.688
3ldl ATP78 kDa glucose-regulated protein / 0.683
4xjc TTPdCTP deaminase / 0.673
3ryh GTPTubulin alpha chain / 0.671
2a84 ATPPantothenate synthetase 6.3.2.1 0.670
2qwn ADPHeat shock cognate 71 kDa protein / 0.668
3bxz ADPProtein translocase subunit SecA / 0.667
4ihj GTPTubulin alpha-1B chain / 0.667
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.666
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.664
2pz8 APCNH(3)-dependent NAD(+) synthetase / 0.664
4dwb 0M7Farnesyl pyrophosphate synthase / 0.663
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.658
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
3wqu ATPCell division protein FtsA / 0.657
1ats ADPHeat shock cognate 71 kDa protein / 0.655
3ldw IPEFarnesyl pyrophosphate synthase, putative / 0.654
4ymv ATPABC-type polar amino acid transport system, ATPase component / 0.653
1qtm TTPDNA polymerase I, thermostable 2.7.7.7 0.652
2r4u ADPGlycogen synthase 2.4.1.21 0.652