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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
3pkaY02Methionine aminopeptidase 2

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3pkaY02Methionine aminopeptidase 2/1.000
3pkdY10Methionine aminopeptidase 2/0.655
3pkbY16Methionine aminopeptidase 2/0.624
3pkeY10Methionine aminopeptidase 2/0.624
4flkY10Methionine aminopeptidase 1/0.560
4iksTFDMethionine aminopeptidase 1/0.549
2g6pHM2Methionine aminopeptidase 1/0.540
2nq7HM5Methionine aminopeptidase 1/0.540
4fllYZ6Methionine aminopeptidase 1/0.536
4fliY16Methionine aminopeptidase 1/0.531
4iktTFVMethionine aminopeptidase 1/0.530
3iu7FCDMethionine aminopeptidase 2/0.527
3iu8T03Methionine aminopeptidase 2/0.514
2gg8U15Methionine aminopeptidase/0.508
1r5gAO1Methionine aminopeptidase 2/0.507
2ggbU17Methionine aminopeptidase/0.501
4ikrPVPMethionine aminopeptidase 1/0.501
4hxx1AYMethionine aminopeptidase 1/0.487
4fljY08Methionine aminopeptidase 1/0.485
2q93B21Methionine aminopeptidase/0.481
2evcFC3Methionine aminopeptidase/0.478
2gg3U13Methionine aminopeptidase/0.476
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.475
3pkcY08Methionine aminopeptidase 2/0.474
2q96A18Methionine aminopeptidase/0.471
2q94A04Methionine aminopeptidase/0.467
2evmFC2Methionine aminopeptidase/0.466
3d27W29Methionine aminopeptidase/0.466
2aouCQAHistamine N-methyltransferase2.1.1.80.465
4ikuSHXMethionine aminopeptidase 1/0.465
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.464
1obnASVIsopenicillin N synthase1.21.3.10.463
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.459
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
1yw8A75Methionine aminopeptidase 2/0.455
2gg9U16Methionine aminopeptidase/0.455
2gg0U11Methionine aminopeptidase/0.454
1c23MPHMethionine aminopeptidase/0.453
2xuqTZ4Acetylcholinesterase3.1.1.70.453
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
4e2yJHZMethyltransferase/0.453
2p98YE7Methionine aminopeptidase/0.452
4bftZVTPantothenate kinase2.7.1.330.452
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.451
2wzySQXSoluble acetylcholine receptor/0.451
2jf0HBPAcetylcholinesterase3.1.1.70.450
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.449
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
1qzyTDEMethionine aminopeptidase 2/0.448
1r5hAO2Methionine aminopeptidase 2/0.448
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.446
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.446
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.445
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.445
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.445
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4q0kGA3Phytohormone-binding protein/0.445
2qimZEAClass 10 plant pathogenesis-related protein/0.444
2xukTZ5Acetylcholinesterase3.1.1.70.444
1odcA8BAcetylcholinesterase3.1.1.70.443
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.442
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.442
2gg2U12Methionine aminopeptidase/0.442
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.441
4ey7E20Acetylcholinesterase3.1.1.70.441
2g1s4IGRenin3.4.23.150.440
3m4p4ADAsparaginyl-tRNA synthetase, putative/0.440