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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
5bsm ATP 4-coumarate--CoA ligase 2 6.2.1.12

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5bsm ATP4-coumarate--CoA ligase 2 6.2.1.12 1.351
3fce ATPD-alanine--poly(phosphoribitol) ligase subunit 1 / 0.835
3fcc ATPD-alanine--poly(phosphoribitol) ligase subunit 1 / 0.750
2q36 ATPActin, alpha skeletal muscle / 0.736
1v25 ANPLong-chain-fatty-acid--CoA ligase 6.2.1.3 0.735
4cbx ATPActin-2 / 0.732
3ffk ATPActin, alpha skeletal muscle / 0.721
4pki ATPActin, alpha skeletal muscle / 0.718
1s22 ATPActin, alpha skeletal muscle / 0.717
3eks ATPActin-5C / 0.716
3m1f ATPActin, alpha skeletal muscle / 0.704
5ce3 ATPActin / 0.704
3mn9 ATPActin-5C / 0.703
1eqy ATPActin, alpha skeletal muscle / 0.702
4pkg ATPActin, alpha skeletal muscle / 0.702
1c0f ATPMajor actin / 0.688
3tu5 ATPActin, alpha skeletal muscle / 0.688
3mn7 ATPActin-5C / 0.685
4b1v ATPActin, alpha skeletal muscle / 0.682
4pl8 ATPActin, alpha skeletal muscle / 0.682
3a5o ATPMajor actin / 0.680
3m6g ATPActin, alpha skeletal muscle / 0.679
3w3d ATPActin, gamma-enteric smooth muscle / 0.676
4to3 DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.676
2w5a ADPSerine/threonine-protein kinase Nek2 2.7.11.1 0.675
3daw ATPActin, alpha skeletal muscle / 0.675
2x60 GTPMannose-1-phosphate guanylyltransferase / 0.674
5ifi PRXAcetyl-coenzyme A synthetase / 0.674
3dyh 721Farnesyl pyrophosphate synthase / 0.673
5bur ATP2-succinylbenzoate--CoA ligase / 0.670
1rfq ATPActin, alpha skeletal muscle / 0.669
1rgi ATPActin, alpha skeletal muscle / 0.668
1yv5 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.668
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.667
1wua ATPActin, alpha skeletal muscle / 0.665
2a41 ATPActin, alpha skeletal muscle / 0.664
3a5m ATPMajor actin / 0.664
4ci6 ATPActin / 0.663
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.663
5byl GCPBifunctional AAC/APH 2.3.1 0.663
5i4n ATPTyrosine-protein kinase JAK2 / 0.663
1zm7 TTPDeoxynucleoside kinase / 0.661
3wt0 ATPCell division protein FtsA / 0.661
4bri UNPEctonucleoside triphosphate diphosphohydrolase I / 0.661
4qfx DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.661
4jhd ANPActin-5C / 0.660
1pg3 PRXAcetyl-coenzyme A synthetase / 0.659
3kxw 1ZZSaframycin Mx1 synthetase B / 0.659
1xje TTPVitamin B12-dependent ribonucleotide reductase / 0.658
2p9k ATPActin-related protein 2 / 0.658
4wud ANPDNA gyrase subunit B / 0.657
3vth APCCarbamoyltransferase / 0.656
4ehu ANP2-hydroxyisocaproyl-CoA dehydratase activator / 0.656
2p2b PRXAcetyl-coenzyme A synthetase / 0.655
2ydo ADNAdenosine receptor A2a / 0.655
3zkd ANPDNA gyrase subunit B / 0.655
4kh0 ATPAspartate carbamoyltransferase regulatory chain {ECO:0000256|HAMAP-Rule:MF_00002} / 0.655
3zcb ATPAdenosine monophosphate-protein transferase VbhT 2.7.7.n1 0.654
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.654
4nu0 AP5Adenylate kinase / 0.653
4eht ADP2-hydroxyisocaproyl-CoA dehydratase activator / 0.652
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.651
1t44 ATPActin, alpha skeletal muscle / 0.650
4brd ANPEctonucleoside triphosphate diphosphohydrolase I / 0.650
4dxj 0M9Farnesyl pyrophosphate synthase / 0.650
4wuc ANPDNA gyrase subunit B / 0.650