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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
4ramPNMMetallo-beta-lactamase type 2

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4ramPNMMetallo-beta-lactamase type 2/1.000
4hl2ZZ7Metallo-beta-lactamase type 2/0.644
4h0dZZ7Metallo-beta-lactamase type 2/0.627
4hl1ZZ7Metallo-beta-lactamase type 2/0.555
4ey20RMMetallo-beta-lactamase type 2/0.535
4eyb0WOMetallo-beta-lactamase type 2/0.533
1jjeBYSBeta-lactamase/0.516
4rawZZ7Metallo-beta-lactamase type 2/0.516
4eyfPNKMetallo-beta-lactamase type 2/0.513
3iogSDFMetallo-beta-lactamase type 2/0.496
4exsX8ZMetallo-beta-lactamase type 2/0.495
2qdsMCOMetallo-beta-lactamase type 2/0.490
1fx9MJIPhospholipase A2, major isoenzyme3.1.1.40.489
1dd6MCIMetallo-beta-lactamase type 2/0.479
2w2lNADD-mandelate dehydrogenase/0.479
1jjtBDSBeta-lactamase/0.476
4c1fX8ZMetallo-beta-lactamase type 2/0.474
1hlk113Metallo-beta-lactamase type 2/0.469
4c1hX8ZMetallo-beta-lactamase type 2/0.464
3akm11DFatty acid-binding protein, intestinal/0.463
4xybNDPFormate dehydrogenase/0.460
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.459
2rd2QSIGlutamine--tRNA ligase6.1.1.180.458
1a8t061Metallo-beta-lactamase type 2/0.456
2e20B4PPropionate kinase/0.456
3nguADPNucleoside diphosphate kinase/0.456
1w29TS06,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
4cf7ADPAdenylate kinase/0.454
2ea4F79Methionine aminopeptidase 2/0.453
2flhZEACytokinin-specific binding protein/0.453
3qh23NMThiazole tautomerase/0.453
2c2aADPSensor histidine kinase/0.452
4q0kGA3Phytohormone-binding protein/0.451
1kvoOAPPhospholipase A2, membrane associated/0.450
1m4dCOAAminoglycoside 2'-N-acetyltransferase2.3.10.450
3a5zKAAElongation factor P--(R)-beta-lysine ligase/0.449
4psbGA3Cytokinin-specific binding protein/0.449
3ogkOGKCoronatine-insensitive protein 1/0.448
4k88HFGBifunctional glutamate/proline--tRNA ligase6.1.1.150.448
1kr3113Metallo-beta-lactamase type 2/0.446
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.446
3kr6UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.446
4d9fDCSD-cysteine desulfhydrase/0.446
4edy9PQHematopoietic prostaglandin D synthase/0.446
4h4qFADBiphenyl dioxygenase ferredoxin reductase subunit/0.446
1x2hLPALipoate-protein ligase A6.3.1.200.445
2gr1FADFerredoxin reductase/0.445
3lu7IPXSerum albumin/0.443
3p3e3P3UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.443
3qj0QI3Botulinum neurotoxin type A3.4.24.690.443
1fxfMJIPhospholipase A2, major isoenzyme3.1.1.40.442
3n2eOSAShikimate kinase2.7.1.710.442
4jyzATPGlutamine--tRNA ligase6.1.1.180.442
1u1f183Uridine phosphorylase2.4.2.30.441
3nglNAPBifunctional protein FolD/0.441
3ntgD72Prostaglandin G/H synthase 21.14.99.10.441
2nnqT4BFatty acid-binding protein, adipocyte/0.440
3ba6AN2Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.440
4p2lFADSulfhydryl oxidase 11.8.3.20.440