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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
2zev B71 Geranylgeranyl pyrophosphate synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2zev B71Geranylgeranyl pyrophosphate synthase / 1.322
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.812
2e91 ZOLGeranylgeranyl pyrophosphate synthase / 0.790
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.775
4h5e YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.762
4h5d YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.761
4dem YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.759
4dwb 0M7Farnesyl pyrophosphate synthase / 0.756
2e95 B75Geranylgeranyl pyrophosphate synthase / 0.747
2o1o RISPutative farnesyl pyrophosphate synthase / 0.747
3dyh 721Farnesyl pyrophosphate synthase / 0.737
2z7h GG3Geranylgeranyl pyrophosphate synthase / 0.735
4h5c YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.723
4dxj 0M9Farnesyl pyrophosphate synthase / 0.721
4q23 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.719
2z78 H86Geranylgeranyl pyrophosphate synthase / 0.716
2bc9 GNPGuanylate-binding protein 1 / 0.715
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.714
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.714
4kqs RISFarnesyl pyrophosphate synthase 2.5.1.10 0.713
1zw5 ZOLFarnesyl pyrophosphate synthase 2.5.1.10 0.706
3ldw ZOLFarnesyl pyrophosphate synthase, putative / 0.703
3krf DSTGeranyl diphosphate synthase large subunit / 0.689
4nke RISFarnesyl pyrophosphate synthase 2.5.1.10 0.688
2z4w 749Geranylgeranyl pyrophosphate synthase / 0.681
2ywv ADPPhosphoribosylaminoimidazole-succinocarboxamide synthase / 0.677
2z52 H23Geranylgeranyl pyrophosphate synthase / 0.676
5ero 210Fusicoccadiene synthase 2.5.1.29 0.675
4to1 DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.672
2z4z SC0Geranylgeranyl pyrophosphate synthase / 0.671
2y6p CTP3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 0.670
4x2d ATPFic family protein putative filamentation induced by cAMP protein / 0.670
1z5c ADPType 2 DNA topoisomerase 6 subunit B / 0.667
5i4n ATPTyrosine-protein kinase JAK2 / 0.666
3dl0 AP5Adenylate kinase / 0.665
3ryw K9HFarnesyl pyrophosphate synthase, putative / 0.665
1mx0 ANPType 2 DNA topoisomerase 6 subunit B / 0.663
1x09 IPEDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) 2.5.1.31 0.663
2cvu ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.660
5erm 210Fusicoccadiene synthase 4.2.3.43 0.659
2zet GTPRas-related protein Rab-27B / 0.658
4fvq ATPTyrosine-protein kinase JAK2 / 0.658
1lot ATPActin, alpha skeletal muscle / 0.657
3ncq ATPNitrogen regulatory protein P-II (GlnB-2) / 0.657
4brd ANPEctonucleoside triphosphate diphosphohydrolase I / 0.657
4u0s ADPAdenosine monophosphate-protein transferase FICD 2.7.7.n1 0.656
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.655
1tu3 GNPRas-related protein Rab-5A / 0.655
4brg GNPEctonucleoside triphosphate diphosphohydrolase I / 0.655
4bri UNPEctonucleoside triphosphate diphosphohydrolase I / 0.655
4psg NOHThymidylate synthase / 0.655
2gqr ADPPhosphoribosylaminoimidazole-succinocarboxamide synthase 6.3.2.6 0.654
2gr0 ADPFerredoxin reductase / 0.653
4irr UMPThymidylate synthase / 0.653
4y9u FADNADPH--cytochrome P450 reductase / 0.653
5dif GNPGTP-binding nuclear protein Ran / 0.653
4y7c FADNADPH--cytochrome P450 reductase / 0.652
3tut ATPRNA 3'-terminal phosphate cyclase 6.5.1.4 0.651
4ee3 UDHBeta-1,4-galactosyltransferase 1 / 0.650