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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
4mgkCMPRap guanine nucleotide exchange factor 4

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4mgkCMPRap guanine nucleotide exchange factor 4/1.000
4mgiCMPRap guanine nucleotide exchange factor 4/0.490
1db1VDXVitamin D3 receptor/0.484
2znoS44Peroxisome proliferator-activated receptor gamma/0.479
4ambDUDPutative glycosyl transferase/0.478
4o2bLOCTubulin beta-2B chain/0.475
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.471
4b7sQLECytochrome P450 monooxygenase PikC/0.470
4l9kEHFSerum albumin/0.470
3syiFADSulfide-quinone reductase/0.469
2c27ACOMycothiol acetyltransferase2.3.1.1890.466
1rm5NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.464
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.462
1txiTX5Vitamin D3 receptor/0.462
4tuvCPZCytochrome P450 1191.140.462
1j39UPGDNA beta-glucosyltransferase/0.461
2q59240Peroxisome proliferator-activated receptor gamma/0.461
4f9mFCMPeroxisome proliferator-activated receptor gamma/0.461
1fm6BRLPeroxisome proliferator-activated receptor gamma/0.460
1rx8FOLDihydrofolate reductase1.5.1.30.460
1lsoNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.459
4fhh0U3Vitamin D3 receptor A/0.459
4itfTFYVitamin D3 receptor/0.459
2fzwNADAlcohol dehydrogenase class-31.1.1.10.458
4h4uNDPBiphenyl dioxygenase ferredoxin reductase subunit/0.457
1ie8KH1Vitamin D3 receptor/0.456
2om9AJAPeroxisome proliferator-activated receptor gamma/0.456
2pobGW4Peroxisome proliferator-activated receptor gamma/0.456
1bwsNDPGDP-L-fucose synthase/0.455
1fm7DFVChalcone--flavonone isomerase 15.5.1.60.455
3v9y24LPeroxisome proliferator-activated receptor gamma/0.455
1e7qNAPGDP-L-fucose synthase/0.454
3a1nNADNDP-sugar epimerase/0.454
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.454
4ki8ADP60 kDa chaperonin/0.454
5eypLOCTubulin beta chain/0.454
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.453
2uuvFADAlkyldihydroxyacetonephosphate synthase2.5.1.260.453
3t2yFADSulfide-quinone reductase/0.453
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.452
5hsaFASAlcohol oxidase 11.1.3.130.452
2iyaZIOOleandomycin glycosyltransferase/0.451
5itzLOCTubulin beta-2B chain/0.451
1fxsNAPGDP-L-fucose synthase/0.449
1jipKTN6-deoxyerythronolide B hydroxylase/0.449
2pswCOAN-alpha-acetyltransferase 50/0.449
3qlfPD5Proto-oncogene tyrosine-protein kinase Src2.7.10.20.449
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.448
1y0s331Peroxisome proliferator-activated receptor delta/0.448
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.448
3atzFMNProstaglandin F2a synthase/0.448
3w5rLOAVitamin D3 receptor/0.448
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.448
1k6cMK1Gag-Pol polyprotein3.4.23.160.447
3a8tATPAdenylate isopentenyltransferase/0.447
3bbrBHYGlutamate receptor 2/0.447
3kpkFADSulfide-quinone reductase/0.447
3r5yF42Uncharacterized protein/0.447
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.447
4xldBRLPeroxisome proliferator-activated receptor gamma/0.447
4z07PCGcGMP-dependent protein kinase 12.7.11.120.447
5a3cNADSIR2 family protein/0.447
1cydNDPCarbonyl reductase [NADPH] 21.1.1.1840.446
1fm9570Peroxisome proliferator-activated receptor gamma/0.446
2bi4NADLactaldehyde reductase1.1.1.770.446
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.446
2q61SF1Peroxisome proliferator-activated receptor gamma/0.446
3nbvANPKetohexokinase/0.446
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.446
4fc7NAPPeroxisomal 2,4-dienoyl-CoA reductase1.3.1.340.446
4o701QKBromodomain-containing protein 4/0.446
4okx198Androgen receptor/0.446
1ia4TQ6Dihydrofolate reductase1.5.1.30.445
1uzwCDHIsopenicillin N synthase1.21.3.10.445
3cifNADGlyceraldehyde-3-phosphate dehydrogenase/0.445
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
3h3sH15Collagen type IV alpha-3-binding protein/0.445
3vspEK8Peroxisome proliferator-activated receptor gamma/0.445
3vt7VDXVitamin D3 receptor/0.445
4iteTEYVitamin D3 receptor/0.445
4q71FADBifunctional protein PutA/0.445
1fwkADPHomoserine kinase2.7.1.390.444
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.444
2jb4A14Isopenicillin N synthase1.21.3.10.444
2vcmM11Isopenicillin N synthase1.21.3.10.444
3l0lHC3Nuclear receptor ROR-gamma/0.444
3nwq2NCGag-Pol polyprotein3.4.23.160.444
3t2zFADSulfide-quinone reductase/0.444
4mxxDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.444
4nxwADPMitochondrial dynamics protein MID51/0.444
1bk0ACVIsopenicillin N synthase1.21.3.10.443
1dhiMTXDihydrofolate reductase1.5.1.30.443
1nzdUPGDNA beta-glucosyltransferase/0.443
1qjfACSIsopenicillin N synthase1.21.3.10.443
2hwrDRDPeroxisome proliferator-activated receptor gamma/0.443
2nnhREACytochrome P450 2C8/0.443
3vrwYS5Vitamin D3 receptor/0.443
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.443
4fhi0S4Vitamin D3 receptor A/0.443
4uyf73BBromodomain-containing protein 2/0.443
1hvyD16Thymidylate synthase2.1.1.450.442
1pr9NAPL-xylulose reductase1.1.1.100.442
2ath3EAPeroxisome proliferator-activated receptor gamma/0.442
2vxoXMPGMP synthase [glutamine-hydrolyzing]6.3.5.20.442
3b70NAPEnoyl reductase LovC10.442
3mdmFJZCholesterol 24-hydroxylase/0.442
3w2eNADNADH-cytochrome b5 reductase 31.6.2.20.442
4bcmT7ZCyclin-dependent kinase 22.7.11.220.442
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4rupH97Vitamin D3 receptor A/0.442
4v12POGMaoC like domain protein/0.442
5iw5NMNNADH pyrophosphatase/0.442
1f8fNADBenzyl alcohol dehydrogenase/0.441
1g4tFTPThiamine-phosphate synthase/0.441
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
2henADPEphrin type-B receptor 22.7.10.10.441
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.441
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.441
3zk5Z18Cytochrome P450 monooxygenase PikC/0.441
5bsfNADPyrroline-5-carboxylate reductase/0.441
1eupASD6-deoxyerythronolide B hydroxylase/0.440
2dfvNADL-threonine 3-dehydrogenase/0.440
2hfpNSIPeroxisome proliferator-activated receptor gamma/0.440
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.440
3gwfFADCyclohexanone monooxygenase/0.440
3hk1B64Fatty acid-binding protein, adipocyte/0.440
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.440
3r9uFADThioredoxin reductase/0.440
4kqwNAPKetol-acid reductoisomerase (NADP(+))/0.440